Commands, Arguments, Options

Note

All subcommands, arguments, and options listed in these documents can be printed, along with a short explanation of each, on the command line by running seismic [command(s)] --help. For example, seismic --help prints all options and subcommands for the command seismic, seismic graph --help prints all options and subcommands for the command seismic graph, and seismic graph profile --help prints all options and subcommands for the command seismic graph profile.

Run the entire workflow

seismic wf

Run the entire workflow.

seismic wf [OPTIONS] FASTA [INPUT_PATH]...

Options

--demult-on, --demult-off

Enable demultiplexing

-x, --fastqx <fastqx>

FASTQ files of paired-end reads with mates 1 and 2 in separate files

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

--barcode-start <barcode_start>

Index of start of barcode

--barcode-end <barcode_end>

Length of barcode

-o, --out-dir <out_dir>

Write all output files to this directory

--parallel-demultiplexing <parallel_demultiplexing>

Whether to run demultiplexing at maximum speed by submitting multithreaded grep functions

--clipped <clipped>

Designates the amount of clipped patterns to search for in the sample, will raise compution time

--mismatch-tolerence <mismatch_tolerence>

Designates the allowable amount of mismatches allowed in a string and still be considered a valid pattern find. will increase non-parallel computation at a factorial rate. use caution going above 2 mismatches. does not apply to clipped sequences.

--index-tolerance <index_tolerance>

Designates the allowable amount of distance you allow the pattern to be found in a read from the reference index

--demulti-overwrite <demulti_overwrite>

Desiginates whether to overwrite the grepped fastq. should only be used if changing setting on the same sample

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-R, --refs-meta <refs_meta>

Add reference metadata from this CSV file to exported results

-y, --fastqy <fastqy>

FASTQ file(s) of paired-end reads with mates 1 and 2 interleaved

-z, --fastqz <fastqz>

FASTQ file(s) of single-end reads

-X, --dmfastqx <dmfastqx>

Demultiplexed FASTQ files of mate 1 and mate 2 reads

-Y, --dmfastqy <dmfastqy>

Demultiplexed FASTQ files of paired-end reads interleaved in one file

-Z, --dmfastqz <dmfastqz>

Demultiplexed FASTQ files of single-end reads

--fastp, --no-fastp

Use fastp to QC, filter, and trim reads before alignment

--fastp-5, --no-fastp-5

Trim low-quality bases from the 5’ ends of reads

--fastp-3, --no-fastp-3

Trim low-quality bases from the 3’ ends of reads

--fastp-w <fastp_w>

Use this window size (nt) for –fastp-5 and –fastp-3

--fastp-m <fastp_m>

Use this mean quality threshold for –fastp-5 and –fastp-3

--fastp-poly-g <fastp_poly_g>

Trim poly(G) tails (two-color sequencing artifacts) from the 3’ end

Options:

yes | no | auto

--fastp-poly-g-min-len <fastp_poly_g_min_len>

Minimum number of Gs to consider a poly(G) tail for –fastp-poly-g

--fastp-poly-x, --no-fastp-poly-x

Trim poly(X) tails (i.e. of any nucleotide) from the 3’ end

--fastp-poly-x-min-len <fastp_poly_x_min_len>

Minimum number of bases to consider a poly(X) tail for –fastp-poly-x

--fastp-adapter-trimming, --no-fastp-adapter-trimming

Trim adapter sequences from the 3’ ends of reads

--fastp-adapter-1 <fastp_adapter_1>

Trim this adapter sequence from the 3’ ends of read 1s

--fastp-adapter-2 <fastp_adapter_2>

Trim this adapter sequence from the 3’ ends of read 2s

--fastp-adapter-fasta <fastp_adapter_fasta>

Trim adapter sequences in this FASTA file from the 3’ ends of reads

--fastp-detect-adapter-for-pe, --no-fastp-detect-adapter-for-pe

Automatically detect the adapter sequences for paired-end reads

--fastp-min-length <fastp_min_length>

Discard reads shorter than this length

--bt2-local, --bt2-end-to-end

Align reads in local mode rather than end-to-end mode

--bt2-discordant, --bt2-no-discordant

Output paired-end reads whose mates align discordantly

--bt2-mixed, --bt2-no-mixed

Attempt to align individual mates of pairs that fail to align

--bt2-dovetail, --bt2-no-dovetail

Consider dovetailed mate pairs to align concordantly

--bt2-contain, --bt2-no-contain

Consider nested mate pairs to align concordantly

--bt2-I <bt2_i>

Discard paired-end alignments shorter than this many bases

--bt2-X <bt2_x>

Discard paired-end alignments longer than this many bases

--bt2-score-min-e2e <bt2_score_min_e2e>

Discard alignments that score below this threshold in end-to-end mode

--bt2-score-min-loc <bt2_score_min_loc>

Discard alignments that score below this threshold in local mode

--bt2-i <bt2_s>

Seed Bowtie2 alignments at this interval

--bt2-L <bt2_l>

Use this seed length for Bowtie2

--bt2-gbar <bt2_gbar>

Do not place gaps within this many bases from the end of a read

--bt2-D <bt2_d>

Discard alignments if over this many consecutive seed extensions fail

--bt2-R <bt2_r>

Re-seed reads with repetitive seeds up to this many times

--bt2-dpad <bt2_dpad>

Pad the alignment matrix with this many bases (to allow gaps)

--bt2-orient <bt2_orient>

Require paired mates to have this orientation

Options:

fr | rf | ff

--bt2-un, --bt2-no-un

Output unaligned reads to a FASTQ file

--min-mapq <min_mapq>

Discard reads with mapping qualities below this threshold

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--sep-strands, --mix-strands

Separate each alignment map into forward- and reverse-strand reads

--f1r2-fwd, --f1r2-rev

With –sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded

--rev-label <rev_label>

With –sep-strands, add this label to each reverse-strand reference

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

--min-phred <min_phred>

Mark base calls with Phred scores lower than this threshold as ambiguous

--batch-size <batch_size>

Limit batches to at most this many reads

--insert3, --insert5

Mark each insertion on the base to its 3’ (True) or 5’ (False) side

--ambindel, --no-ambindel

Mark all ambiguous insertions and deletions (indels)

--overhangs, --no-overhangs

Retain the overhangs of paired-end mates that dovetail

-5, --clip-end5 <clip_end5>

Clip this many bases from the 5’ end of each read

-3, --clip-end3 <clip_end3>

Clip this many bases from the 3’ end of each read

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--write-read-names, --no-write-read-names

Write the name of each read in a second set of batches (necessary for the options –mask-read or –mask-read-file)

--relate-pos-table, --no-relate-pos-table

Tabulate relationships per position for relate data

--relate-read-table, --no-relate-read-table

Tabulate relationships per read for relate data

--relate-cx, --relate-py

Use a fast (C extension module) version of the relate algorithm; the slow (Python) version is still avilable as a fallback if the C extension cannot be loaded, and for debugging/benchmarking

-c, --mask-coords <mask_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --mask-primers <mask_primers>

Select a region of a reference given its forward and reverse primers

--primer-gap <primer_gap>

Leave a gap of this many bases between the primer and the region

-i, --mask-regions-file <mask_regions_file>

Select regions of references from coordinates/primers in a CSV file

--mask-del, --keep-del

Mask deletions

--mask-ins, --keep-ins

Mask insertions

--mask-mut <mask_mut>

Mask this type of mutation

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables)

--mask-gu, --keep-gu

Mask G and U bases

--mask-pos <mask_pos>

Mask this position in this reference

--mask-pos-file <mask_pos_file>

Mask positions in references from a file

--min-ninfo-pos <min_ninfo_pos>

Mask positions with fewer than this many informative base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--mask-read <mask_read>

Mask the read with this name

--mask-read-file <mask_read_file>

Mask the reads with names in this file

--mask-discontig, --keep-discontig

Mask paired-end reads with discontiguous mates

--min-ncov-read <min_ncov_read>

Mask reads with fewer than this many bases covering the region

--min-finfo-read <min_finfo_read>

Mask reads with less than this fraction of informative base calls

--max-fmut-read <max_fmut_read>

Mask reads with more than this fraction of mutated base calls

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--quick-unbias, --exact-unbias

Correct observer bias using a quick (typically linear time) heuristic

--quick-unbias-thresh <quick_unbias_thresh>

Treat mutated fractions under this threshold as 0 with –quick-unbias

--max-mask-iter <max_mask_iter>

Stop masking after this many iterations (0 for no limit)

--mask-pos-table, --no-mask-pos-table

Tabulate relationships per position for mask data

--mask-read-table, --no-mask-read-table

Tabulate relationships per read for mask data

--cluster, --no-cluster

Cluster reads to find alternative structures

--min-clusters <min_clusters>

Start at this many clusters

-k, --max-clusters <max_clusters>

Stop at this many clusters (0 for no limit)

-e, --em-runs <em_runs>

Run EM this many times for each number of clusters (K) except K = 1

--em-thresh <em_thresh>

Stop EM when the log likelihood increases by less than this threshold

--min-em-iter <min_em_iter>

Run EM for at least this many iterations (times number of clusters)

--max-em-iter <max_em_iter>

Run EM for at most this many iterations (times number of clusters)

--max-pearson-run <max_pearson_run>

Remove runs with two clusters more similar than this correlation

--min-marcd-run <min_marcd_run>

Remove runs with two clusters different by less than this MARCD

--jackpot, --no-jackpot

Calculate the jackpotting quotient to find over-represented reads

--jackpot-conf-level <jackpot_conf_level>

Confidence level for the jackpotting quotient confidence interval

--max-jackpot-quotient <max_jackpot_quotient>

Remove runs whose jackpotting quotient exceeds this limit

--max-loglike-vs-best <max_loglike_vs_best>

Remove Ks with a log likelihood gap larger than this (0 for no limit)

--min-pearson-vs-best <min_pearson_vs_best>

Remove Ks where every run has less than this correlation vs. the best

--max-marcd-vs-best <max_marcd_vs_best>

Remove Ks where every run has more than this MARCD vs. the best

--try-all-ks, --stop-best-k

Try all numbers of clusters (Ks), even after finding the best number

--write-all-ks, --write-best-k

Write all numbers of clusters (Ks), rather than only the best number

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--fold, --no-fold

Predict the secondary structure using the RNAstructure Fold program

-f, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-full, --fold-table

If no regions are specified, whether to default to the full region or to the table’s region

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--fold-temp <fold_temp>

Predict structures at this temperature (Kelvin)

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

--draw, --no-draw

Draw secondary structures with RNArtist.

--struct-num <struct_num>

Draw the specified structure (zero-indexed) or -1 for all structures. By default, draw the structure with the best AUROC.

--color, --no-color

Color bases by their reactivity

--export, --no-export

Export each sample to SEISMICgraph (https://seismicrna.org)

-S, --samples-meta <samples_meta>

Add sample metadata from this CSV file to exported results

--all-pos, --unmasked-pos

Export all positions (not just unmasked positions)

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--hist-bins <hist_bins>

Number of bins in each histogram; must be ≥ 1

--hist-margin <hist_margin>

Autofill margins of at most this width in histograms of ratios

--struct-file <struct_file>

Compare mutational profiles to the structure(s) in this CT file

-w, --window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--graph-mprof, --no-graph-mprof

Graph mutational profiles

--graph-tmprof, --no-graph-tmprof

Graph typed mutational profiles

--graph-ncov, --no-graph-ncov

Graph coverages per position

--graph-mhist, --no-graph-mhist

Graph histograms of mutations per read

--graph-abundance, --no-graph-abundance

Graph abundance of each cluster

--graph-giniroll, --no-graph-giniroll

Graph rolling Gini coefficients

--graph-roc, --no-graph-roc

Graph receiver operating characteristic curves

--graph-aucroll, --no-graph-aucroll

Graph rolling areas under receiver operating characteristic curves

--graph-poscorr, --no-graph-poscorr

Graph phi correlations between positions

--graph-mutdist, --no-graph-mutdist

Graph distances between mutations

--mutdist-null, --no-mutdist-null

Include the null distribution of distances between mutations

Arguments

FASTA

Required argument

INPUT_PATH

Optional argument(s)

Run individual steps of the workflow

seismic demult

Split multiplexed FASTQ files by their barcodes.

seismic demult [OPTIONS] FASTA

Options

-x, --fastqx <fastqx>

FASTQ files of paired-end reads with mates 1 and 2 in separate files

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

--barcode-start <barcode_start>

Index of start of barcode

--barcode-end <barcode_end>

Length of barcode

-o, --out-dir <out_dir>

Write all output files to this directory

--parallel-demultiplexing <parallel_demultiplexing>

Whether to run demultiplexing at maximum speed by submitting multithreaded grep functions

--clipped <clipped>

Designates the amount of clipped patterns to search for in the sample, will raise compution time

--mismatch-tolerence <mismatch_tolerence>

Designates the allowable amount of mismatches allowed in a string and still be considered a valid pattern find. will increase non-parallel computation at a factorial rate. use caution going above 2 mismatches. does not apply to clipped sequences.

--index-tolerance <index_tolerance>

Designates the allowable amount of distance you allow the pattern to be found in a read from the reference index

--demulti-overwrite <demulti_overwrite>

Desiginates whether to overwrite the grepped fastq. should only be used if changing setting on the same sample

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-R, --refs-meta <refs_meta>

Add reference metadata from this CSV file to exported results

Arguments

FASTA

Required argument

seismic align

Trim FASTQ files and align them to reference sequences.

seismic align [OPTIONS] FASTA

Options

-x, --fastqx <fastqx>

FASTQ files of paired-end reads with mates 1 and 2 in separate files

-y, --fastqy <fastqy>

FASTQ file(s) of paired-end reads with mates 1 and 2 interleaved

-z, --fastqz <fastqz>

FASTQ file(s) of single-end reads

-X, --dmfastqx <dmfastqx>

Demultiplexed FASTQ files of mate 1 and mate 2 reads

-Y, --dmfastqy <dmfastqy>

Demultiplexed FASTQ files of paired-end reads interleaved in one file

-Z, --dmfastqz <dmfastqz>

Demultiplexed FASTQ files of single-end reads

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--fastp, --no-fastp

Use fastp to QC, filter, and trim reads before alignment

--fastp-5, --no-fastp-5

Trim low-quality bases from the 5’ ends of reads

--fastp-3, --no-fastp-3

Trim low-quality bases from the 3’ ends of reads

--fastp-w <fastp_w>

Use this window size (nt) for –fastp-5 and –fastp-3

--fastp-m <fastp_m>

Use this mean quality threshold for –fastp-5 and –fastp-3

--fastp-poly-g <fastp_poly_g>

Trim poly(G) tails (two-color sequencing artifacts) from the 3’ end

Options:

yes | no | auto

--fastp-poly-g-min-len <fastp_poly_g_min_len>

Minimum number of Gs to consider a poly(G) tail for –fastp-poly-g

--fastp-poly-x, --no-fastp-poly-x

Trim poly(X) tails (i.e. of any nucleotide) from the 3’ end

--fastp-poly-x-min-len <fastp_poly_x_min_len>

Minimum number of bases to consider a poly(X) tail for –fastp-poly-x

--fastp-adapter-trimming, --no-fastp-adapter-trimming

Trim adapter sequences from the 3’ ends of reads

--fastp-adapter-1 <fastp_adapter_1>

Trim this adapter sequence from the 3’ ends of read 1s

--fastp-adapter-2 <fastp_adapter_2>

Trim this adapter sequence from the 3’ ends of read 2s

--fastp-adapter-fasta <fastp_adapter_fasta>

Trim adapter sequences in this FASTA file from the 3’ ends of reads

--fastp-detect-adapter-for-pe, --no-fastp-detect-adapter-for-pe

Automatically detect the adapter sequences for paired-end reads

--fastp-min-length <fastp_min_length>

Discard reads shorter than this length

--bt2-local, --bt2-end-to-end

Align reads in local mode rather than end-to-end mode

--bt2-discordant, --bt2-no-discordant

Output paired-end reads whose mates align discordantly

--bt2-mixed, --bt2-no-mixed

Attempt to align individual mates of pairs that fail to align

--bt2-dovetail, --bt2-no-dovetail

Consider dovetailed mate pairs to align concordantly

--bt2-contain, --bt2-no-contain

Consider nested mate pairs to align concordantly

--bt2-I <bt2_i>

Discard paired-end alignments shorter than this many bases

--bt2-X <bt2_x>

Discard paired-end alignments longer than this many bases

--bt2-score-min-e2e <bt2_score_min_e2e>

Discard alignments that score below this threshold in end-to-end mode

--bt2-score-min-loc <bt2_score_min_loc>

Discard alignments that score below this threshold in local mode

--bt2-i <bt2_s>

Seed Bowtie2 alignments at this interval

--bt2-L <bt2_l>

Use this seed length for Bowtie2

--bt2-gbar <bt2_gbar>

Do not place gaps within this many bases from the end of a read

--bt2-D <bt2_d>

Discard alignments if over this many consecutive seed extensions fail

--bt2-R <bt2_r>

Re-seed reads with repetitive seeds up to this many times

--bt2-dpad <bt2_dpad>

Pad the alignment matrix with this many bases (to allow gaps)

--bt2-orient <bt2_orient>

Require paired mates to have this orientation

Options:

fr | rf | ff

--bt2-un, --bt2-no-un

Output unaligned reads to a FASTQ file

--min-mapq <min_mapq>

Discard reads with mapping qualities below this threshold

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--sep-strands, --mix-strands

Separate each alignment map into forward- and reverse-strand reads

--f1r2-fwd, --f1r2-rev

With –sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded

--rev-label <rev_label>

With –sep-strands, add this label to each reverse-strand reference

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

FASTA

Required argument

seismic relate

Compute relationships between references and aligned reads.

seismic relate [OPTIONS] FASTA [INPUT_PATH]...

Options

--sep-strands, --mix-strands

Separate each alignment map into forward- and reverse-strand reads

--rev-label <rev_label>

With –sep-strands, add this label to each reverse-strand reference

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--min-mapq <min_mapq>

Discard reads with mapping qualities below this threshold

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

--min-phred <min_phred>

Mark base calls with Phred scores lower than this threshold as ambiguous

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--batch-size <batch_size>

Limit batches to at most this many reads

--insert3, --insert5

Mark each insertion on the base to its 3’ (True) or 5’ (False) side

--ambindel, --no-ambindel

Mark all ambiguous insertions and deletions (indels)

--overhangs, --no-overhangs

Retain the overhangs of paired-end mates that dovetail

-5, --clip-end5 <clip_end5>

Clip this many bases from the 5’ end of each read

-3, --clip-end3 <clip_end3>

Clip this many bases from the 3’ end of each read

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--write-read-names, --no-write-read-names

Write the name of each read in a second set of batches (necessary for the options –mask-read or –mask-read-file)

--relate-pos-table, --no-relate-pos-table

Tabulate relationships per position for relate data

--relate-read-table, --no-relate-read-table

Tabulate relationships per read for relate data

--relate-cx, --relate-py

Use a fast (C extension module) version of the relate algorithm; the slow (Python) version is still avilable as a fallback if the C extension cannot be loaded, and for debugging/benchmarking

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

--keep-tmp, --erase-tmp

Keep temporary files after finishing

Arguments

FASTA

Required argument

INPUT_PATH

Optional argument(s)

seismic mask

Define mutations and regions to filter reads and positions.

seismic mask [OPTIONS] [INPUT_PATH]...

Options

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-c, --mask-coords <mask_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --mask-primers <mask_primers>

Select a region of a reference given its forward and reverse primers

--primer-gap <primer_gap>

Leave a gap of this many bases between the primer and the region

-i, --mask-regions-file <mask_regions_file>

Select regions of references from coordinates/primers in a CSV file

--mask-del, --keep-del

Mask deletions

--mask-ins, --keep-ins

Mask insertions

--mask-mut <mask_mut>

Mask this type of mutation

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables)

--mask-gu, --keep-gu

Mask G and U bases

--mask-pos <mask_pos>

Mask this position in this reference

--mask-pos-file <mask_pos_file>

Mask positions in references from a file

--min-ninfo-pos <min_ninfo_pos>

Mask positions with fewer than this many informative base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--mask-read <mask_read>

Mask the read with this name

--mask-read-file <mask_read_file>

Mask the reads with names in this file

--mask-discontig, --keep-discontig

Mask paired-end reads with discontiguous mates

--min-ncov-read <min_ncov_read>

Mask reads with fewer than this many bases covering the region

--min-finfo-read <min_finfo_read>

Mask reads with less than this fraction of informative base calls

--max-fmut-read <max_fmut_read>

Mask reads with more than this fraction of mutated base calls

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--quick-unbias, --exact-unbias

Correct observer bias using a quick (typically linear time) heuristic

--quick-unbias-thresh <quick_unbias_thresh>

Treat mutated fractions under this threshold as 0 with –quick-unbias

--max-mask-iter <max_mask_iter>

Stop masking after this many iterations (0 for no limit)

--mask-pos-table, --no-mask-pos-table

Tabulate relationships per position for mask data

--mask-read-table, --no-mask-read-table

Tabulate relationships per read for mask data

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic cluster

Infer structure ensembles by clustering reads’ mutations.

seismic cluster [OPTIONS] [INPUT_PATH]...

Options

--min-clusters <min_clusters>

Start at this many clusters

-k, --max-clusters <max_clusters>

Stop at this many clusters (0 for no limit)

-e, --em-runs <em_runs>

Run EM this many times for each number of clusters (K) except K = 1

--em-thresh <em_thresh>

Stop EM when the log likelihood increases by less than this threshold

--min-em-iter <min_em_iter>

Run EM for at least this many iterations (times number of clusters)

--max-em-iter <max_em_iter>

Run EM for at most this many iterations (times number of clusters)

--max-pearson-run <max_pearson_run>

Remove runs with two clusters more similar than this correlation

--min-marcd-run <min_marcd_run>

Remove runs with two clusters different by less than this MARCD

--jackpot, --no-jackpot

Calculate the jackpotting quotient to find over-represented reads

--jackpot-conf-level <jackpot_conf_level>

Confidence level for the jackpotting quotient confidence interval

--max-jackpot-quotient <max_jackpot_quotient>

Remove runs whose jackpotting quotient exceeds this limit

--max-loglike-vs-best <max_loglike_vs_best>

Remove Ks with a log likelihood gap larger than this (0 for no limit)

--min-pearson-vs-best <min_pearson_vs_best>

Remove Ks where every run has less than this correlation vs. the best

--max-marcd-vs-best <max_marcd_vs_best>

Remove Ks where every run has more than this MARCD vs. the best

--try-all-ks, --stop-best-k

Try all numbers of clusters (Ks), even after finding the best number

--write-all-ks, --write-best-k

Write all numbers of clusters (Ks), rather than only the best number

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

Arguments

INPUT_PATH

Optional argument(s)

seismic table

Tabulate counts of relationships per read and position.

seismic table [OPTIONS] [INPUT_PATH]...

Options

--relate-pos-table, --no-relate-pos-table

Tabulate relationships per position for relate data

--relate-read-table, --no-relate-read-table

Tabulate relationships per read for relate data

--mask-pos-table, --no-mask-pos-table

Tabulate relationships per position for mask data

--mask-read-table, --no-mask-read-table

Tabulate relationships per read for mask data

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic fold

Predict RNA secondary structures using mutation rates.

seismic fold [OPTIONS] [INPUT_PATH]...

Options

-f, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-full, --fold-table

If no regions are specified, whether to default to the full region or to the table’s region

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--fold-temp <fold_temp>

Predict structures at this temperature (Kelvin)

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic graph

seismic graph profile

Bar graph of relationships(s) per position.

seismic graph profile [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph delprof

Bar graph of differences between two profiles per position.

seismic graph delprof [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--comppair, --no-comppair

Compare every pair of table files

--compself, --no-compself

Compare every table file with itself

-o, --out-dir <out_dir>

Write all output files to this directory

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph scatter

Scatter plot comparing two profiles.

seismic graph scatter [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--comppair, --no-comppair

Compare every pair of table files

--compself, --no-compself

Compare every table file with itself

-o, --out-dir <out_dir>

Write all output files to this directory

-m, --metric <metric>

Metric to compare mutation rates: ‘pcc’ = Pearson correlation coefficient (r), ‘scc’ = Spearman correlation coefficient (ρ), ‘r2’ = coefficient of determination (R²), ‘marcd’ = mean arcsine distance (MARCD)

Options:

marcd | pcc | scc | r2

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph corroll

Rolling correlation/comparison of two profiles.

seismic graph corroll [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

-w, --window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--comppair, --no-comppair

Compare every pair of table files

--compself, --no-compself

Compare every table file with itself

-o, --out-dir <out_dir>

Write all output files to this directory

-m, --metric <metric>

Metric to compare mutation rates: ‘pcc’ = Pearson correlation coefficient (r), ‘scc’ = Spearman correlation coefficient (ρ), ‘r2’ = coefficient of determination (R²), ‘marcd’ = mean arcsine distance (MARCD)

Options:

marcd | pcc | scc | r2

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph histpos

Histogram of relationship(s) per position.

seismic graph histpos [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--hist-bins <hist_bins>

Number of bins in each histogram; must be ≥ 1

--hist-margin <hist_margin>

Autofill margins of at most this width in histograms of ratios

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph histread

Histogram of relationship(s) per read.

seismic graph histread [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--hist-bins <hist_bins>

Number of bins in each histogram; must be ≥ 1

--hist-margin <hist_margin>

Autofill margins of at most this width in histograms of ratios

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph roc

ROC curve comparing a profile to a structure.

seismic graph roc [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--struct-file <struct_file>

Compare mutational profiles to the structure(s) in this CT file

-f, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-full, --fold-table

If no regions are specified, whether to default to the full region or to the table’s region

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph aucroll

Rolling AUC-ROC comparing a profile to a structure.

seismic graph aucroll [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--struct-file <struct_file>

Compare mutational profiles to the structure(s) in this CT file

-f, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-full, --fold-table

If no regions are specified, whether to default to the full region or to the table’s region

-w, --window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

Extra Utilities

Note

For every extra utility (that is not part of the main workflow), the name begins with +.

seismic listpos

List positions meeting specific criteria.

seismic listpos [OPTIONS] [INPUT_PATH]...

Options

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--complement, --no-complement

List the complement

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic cleanfa

Clean the names and sequences in FASTA files.

seismic cleanfa [OPTIONS] [INPUT_PATH]...

Options

--inplace, --no-inplace

Modify files in-place instead of writing new files (CAUTION: you cannot recover the original files afterwards)

-o, --out-dir <out_dir>

Write all output files to this directory

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic renumct

Renumber connectivity table (CT) files given a 5’ position.

seismic renumct [OPTIONS]

Options

-c, --ct-pos-5 <ct_pos_5>

Connectivity table (CT) file or directory of CT files and the 5’ position to assign to each file

--inplace, --no-inplace

Modify files in-place instead of writing new files (CAUTION: you cannot recover the original files afterwards)

-o, --out-dir <out_dir>

Write all output files to this directory

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic test

Run all unit tests.

seismic test [OPTIONS]

Options

-v, --verbose

Log more messages (-v, -vv, or -vvv) on stderr

seismic sim

seismic sim total

Simulate FASTQ files from scratch.

seismic sim total [OPTIONS]

Options

-P, --profile-name <profile_name>

Give the simulated structure and parameters this profile name

-s, --sample <sample>

Give this name to the simulated sample

--paired-end, --single-end

Simulate paired-end or single-end reads

--read-length <read_length>

Simulate reads with this many base calls

--reverse-fraction <reverse_fraction>

Simulate this fraction of reverse-oriented reads

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--fq-gzip, --fq-text

Simulate FASTQ files with gzip compression or as plain text

-n, --num-reads <num_reads>

Simulate this many reads

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

-o, --sim-dir <sim_dir>

Write all simulated files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

-f, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-temp <fold_temp>

Predict structures at this temperature (Kelvin)

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-c, --clust-conc <clust_conc>

Set the concentration parameter for simulating cluster proportions

--center-fmean <center_fmean>

Set the mean read center as a fraction of the region length

--center-fvar <center_fvar>

Set the variance of the read center as a fraction of its maximum

--length-fmean <length_fmean>

Set the mean read length as a fraction of the region length

--length-fvar <length_fvar>

Set the variance of the read length as a fraction of its maximum

-p, --pmut-paired <pmut_paired>

Set the mean rate of each kind of mutation for paired bases

-u, --pmut-unpaired <pmut_unpaired>

Set the mean rate of each kind of mutation for unpaired bases

-v, --vmut-paired <vmut_paired>

Set the relative variance of mutation rates of paired bases

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of unpaired bases

-R, --refs <refs>

Give this name to the file of simulated references

-r, --ref <ref>

Give this name to the simulated reference

-N, --reflen <reflen>

Simulate a reference sequence with this many bases

seismic sim ref

Simulate a FASTA file of a reference sequence.

seismic sim ref [OPTIONS]

Options

-o, --sim-dir <sim_dir>

Write all simulated files to this directory

-R, --refs <refs>

Give this name to the file of simulated references

-r, --ref <ref>

Give this name to the simulated reference

-N, --reflen <reflen>

Simulate a reference sequence with this many bases

--force, --no-force

Force all tasks to run, overwriting any existing output files

seismic sim fold

Simulate secondary structure(s) a reference sequence.

seismic sim fold [OPTIONS] FASTA

Options

-o, --sim-dir <sim_dir>

Write all simulated files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

-P, --profile-name <profile_name>

Give the simulated structure and parameters this profile name

-f, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-temp <fold_temp>

Predict structures at this temperature (Kelvin)

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

Arguments

FASTA

Required argument

seismic sim params

Simulate parameter files.

seismic sim params [OPTIONS]

Options

-i, --ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

-c, --clust-conc <clust_conc>

Set the concentration parameter for simulating cluster proportions

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

--center-fmean <center_fmean>

Set the mean read center as a fraction of the region length

--center-fvar <center_fvar>

Set the variance of the read center as a fraction of its maximum

--length-fmean <length_fmean>

Set the mean read length as a fraction of the region length

--length-fvar <length_fvar>

Set the variance of the read length as a fraction of its maximum

-p, --pmut-paired <pmut_paired>

Set the mean rate of each kind of mutation for paired bases

-u, --pmut-unpaired <pmut_unpaired>

Set the mean rate of each kind of mutation for unpaired bases

-v, --vmut-paired <vmut_paired>

Set the relative variance of mutation rates of paired bases

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of unpaired bases

seismic sim muts

Simulate the rate of each kind of mutation at each position.

seismic sim muts [OPTIONS]

Options

-i, --ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

-p, --pmut-paired <pmut_paired>

Set the mean rate of each kind of mutation for paired bases

-u, --pmut-unpaired <pmut_unpaired>

Set the mean rate of each kind of mutation for unpaired bases

-v, --vmut-paired <vmut_paired>

Set the relative variance of mutation rates of paired bases

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of unpaired bases

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic sim ends

Simulate the proportions of 5’ and 3’ end coordinates.

seismic sim ends [OPTIONS]

Options

-i, --ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

--center-fmean <center_fmean>

Set the mean read center as a fraction of the region length

--center-fvar <center_fvar>

Set the variance of the read center as a fraction of its maximum

--length-fmean <length_fmean>

Set the mean read length as a fraction of the region length

--length-fvar <length_fvar>

Set the variance of the read length as a fraction of its maximum

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic sim clusts

Simulate the proportions of 5’ and 3’ end coordinates.

seismic sim clusts [OPTIONS]

Options

-i, --ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

-c, --clust-conc <clust_conc>

Set the concentration parameter for simulating cluster proportions

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic sim relate

Simulate a Relate dataset.

seismic sim relate [OPTIONS]

Options

-d, --param-dir <param_dir>

Simulate data using parameter files in this directory

-P, --profile-name <profile_name>

Give the simulated structure and parameters this profile name

-s, --sample <sample>

Give this name to the simulated sample

--paired-end, --single-end

Simulate paired-end or single-end reads

--read-length <read_length>

Simulate reads with this many base calls

--reverse-fraction <reverse_fraction>

Simulate this fraction of reverse-oriented reads

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

-n, --num-reads <num_reads>

Simulate this many reads

--batch-size <batch_size>

Limit batches to at most this many reads

--write-read-names, --no-write-read-names

Write the name of each read in a second set of batches (necessary for the options –mask-read or –mask-read-file)

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic sim fastq

Simulate a FASTQ file.

seismic sim fastq [OPTIONS] [INPUT_PATH]...

Options

-d, --param-dir <param_dir>

Simulate data using parameter files in this directory

-P, --profile-name <profile_name>

Give the simulated structure and parameters this profile name

-s, --sample <sample>

Give this name to the simulated sample

--paired-end, --single-end

Simulate paired-end or single-end reads

--read-length <read_length>

Simulate reads with this many base calls

--reverse-fraction <reverse_fraction>

Simulate this fraction of reverse-oriented reads

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--fq-gzip, --fq-text

Simulate FASTQ files with gzip compression or as plain text

-n, --num-reads <num_reads>

Simulate this many reads

--max-procs <max_procs>

Run up to this many processes simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)