API Reference
The arguments for the CLI and Python API are the same. The CLI is just a wrapper around the Python API.
CLI cmds
dreem demultiplex
dreem demultiplex [OPTIONS]
Options
- --fasta <fasta>
FASTA file of all reference sequences in the project
- --fastq1 <fastq1>
FASTQ files of mate 1 paired-end reads
- --fastq2 <fastq2>
FASTQ files of mate 2 paired-end reads
- --library <library>
Library CSV file
- --barcode-start <barcode_start>
index of start of barcode
- --barcode-length <barcode_length>
length of barcode
- --out-dir <out_dir>
Where to output all finished files
- --temp-dir <temp_dir>
Where to write all temporary files
- --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