Align Report

Align Sample Report

Align Sample Report: Fields

Name	Data Type
Sample	str
Branches	dict[str, str]
Seed for the random number generator	int
Use demultiplexed mode	bool
Use paired-end mode	bool
Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files	int
Use fastp to QC, filter, and trim reads before alignment	bool
Trim low-quality bases from the 5’ ends of reads	bool
Trim low-quality bases from the 3’ ends of reads	bool
Use this window size (nt) for –fastp-5 and –fastp-3	int
Use this mean quality threshold for –fastp-5 and –fastp-3	int
Trim poly(G) tails (two-color sequencing artifacts) from the 3’ end	str
Minimum number of Gs to consider a poly(G) tail for –fastp-poly-g	int
Trim poly(X) tails (i.e. of any nucleotide) from the 3’ end	bool
Minimum number of bases to consider a poly(X) tail for –fastp-poly-x	int
Trim adapter sequences from the 3’ ends of reads	bool
Trim this adapter sequence from the 3’ ends of read 1s	str
Trim this adapter sequence from the 3’ ends of read 2s	str
Trim adapter sequences in this FASTA file from the 3’ ends of reads	str
Automatically detect the adapter sequences for paired-end reads	bool
Discard reads shorter than this length	int
Align reads in local mode rather than end-to-end mode	bool
Output paired-end reads whose mates align discordantly	bool
Attempt to align individual mates of pairs that fail to align	bool
Consider dovetailed mate pairs to align concordantly	bool
Consider nested mate pairs to align concordantly	bool
Discard alignments that score below this threshold	str
Discard paired-end alignments shorter than this many bases	int
Discard paired-end alignments longer than this many bases	int
Do not place gaps within this many bases from the end of a read	int
Use this seed length for Bowtie2	int
Seed Bowtie2 alignments at this interval	str
Discard alignments if over this many consecutive seed extensions fail	int
Re-seed reads with repetitive seeds up to this many times	int
Pad the alignment matrix with this many bases (to allow gaps)	int
Require paired mates to have this orientation	str
Output unaligned reads to a FASTQ file	bool
Discard reads with mapping qualities below this threshold	int
Separate each alignment map into forward- and reverse-strand reads	bool
With –sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded	bool
With –sep-strands, add this label to each reverse-strand reference	str
Discard alignment maps with fewer than this many reads	int
Number of reads in the FASTQ file(s)	int
Number of reads after trimming	int
Number of reads after alignment	dict[str, int]
Number of reads after filtering	dict[str, int]
Number of reads aligned to each reference	dict[str, int]
Checksum of the reference fasta (SHA-512)	str
Checksum(s) of the input fastq(s) (SHA-512)	dict[str, str]
Time began	str
Time ended	str
Time taken (minutes)	float
Version of SEISMIC-RNA	str

Align Sample Report: Example

{
    "Sample": "sample1",
    "Branches": {
        "align": ""
    },
    "Seed for the random number generator": null,
    "Use demultiplexed mode": false,
    "Use paired-end mode": true,
    "Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files": 33,
    "Use fastp to QC, filter, and trim reads before alignment": true,
    "Trim low-quality bases from the 5' ends of reads": false,
    "Trim low-quality bases from the 3' ends of reads": true,
    "Use this window size (nt) for --fastp-5 and --fastp-3": 6,
    "Use this mean quality threshold for --fastp-5 and --fastp-3": 25,
    "Trim poly(G) tails (two-color sequencing artifacts) from the 3' end": "auto",
    "Minimum number of Gs to consider a poly(G) tail for --fastp-poly-g": 10,
    "Trim poly(X) tails (i.e. of any nucleotide) from the 3' end": false,
    "Minimum number of bases to consider a poly(X) tail for --fastp-poly-x": 10,
    "Trim adapter sequences from the 3' ends of reads": true,
    "Trim this adapter sequence from the 3' ends of read 1s": "",
    "Trim this adapter sequence from the 3' ends of read 2s": "",
    "Trim adapter sequences in this FASTA file from the 3' ends of reads": null,
    "Automatically detect the adapter sequences for paired-end reads": true,
    "Discard reads shorter than this length": 9,
    "Align reads in local mode rather than end-to-end mode": true,
    "Output paired-end reads whose mates align discordantly": false,
    "Attempt to align individual mates of pairs that fail to align": false,
    "Consider dovetailed mate pairs to align concordantly": false,
    "Consider nested mate pairs to align concordantly": true,
    "Discard alignments that score below this threshold": "L,1,0.8",
    "Discard paired-end alignments shorter than this many bases": 0,
    "Discard paired-end alignments longer than this many bases": 600,
    "Do not place gaps within this many bases from the end of a read": 4,
    "Use this seed length for Bowtie2": 20,
    "Seed Bowtie2 alignments at this interval": "L,1,0.1",
    "Discard alignments if over this many consecutive seed extensions fail": 4,
    "Re-seed reads with repetitive seeds up to this many times": 2,
    "Pad the alignment matrix with this many bases (to allow gaps)": 2,
    "Require paired mates to have this orientation": "fr",
    "Output unaligned reads to a FASTQ file": true,
    "Discard reads with mapping qualities below this threshold": 25,
    "Separate each alignment map into forward- and reverse-strand reads": false,
    "With --sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded": false,
    "With --sep-strands, add this label to each reverse-strand reference": "-rev",
    "Discard alignment maps with fewer than this many reads": 1000,
    "Number of reads in the FASTQ file(s)": 4008,
    "Number of reads after trimming": 4008,
    "Number of reads after alignment": {
        "reads, were paired": 4008,
        "reads, were paired, aligned concordantly 0 times": 372,
        "reads, were paired, aligned concordantly exactly 1 time": 3636,
        "reads, were paired, aligned concordantly >1 times": 0
    },
    "Number of reads after filtering": {
        "paired-end, both mates mapped": 3595,
        "paired-end, one mate unmapped": 0
    },
    "Number of reads aligned to each reference": {
        "myref": 3595
    },
    "Checksum of the reference fasta (SHA-512)": "e4dcaae215ebadadc57010d22d93f4311cdc0bc02fc2f65db558a14b671d898ef8ff541817bf374aa60688627dbb9601581f7b271e60eb80cc36fc0c7dd51882",
    "Checksum(s) of the input fastq(s) (SHA-512)": {
        "fastq1": "a28f7d8cf7856603cee938c0d6a91561063d6eb8a34ebc2d9bee2b9fa8c04f9c528afe8e6b039bb62467bf71a6358d892fc5fdd2bec9e51902a116f67b791a9d",
        "fastq2": "15242a00abef156c10b18bef6717cd2e9b1ee54165d89aa490ea0176e7977d7f24a3c9e12dece493c67a6ab77b9a43f7ad291a60189275266d22a31882ef1046"
    },
    "Time began": "2026-05-31 at 12:53:08",
    "Time ended": "2026-05-31 at 12:53:09",
    "Time taken (minutes)": 0.01,
    "Version of SEISMIC-RNA": "0.25.3"
}

Align Reference Report

Align Reference Report: Fields

Name	Data Type
Sample	str
Branches	dict[str, str]
Reference	str
Seed for the random number generator	int
Use demultiplexed mode	bool
Use paired-end mode	bool
Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files	int
Use fastp to QC, filter, and trim reads before alignment	bool
Trim low-quality bases from the 5’ ends of reads	bool
Trim low-quality bases from the 3’ ends of reads	bool
Use this window size (nt) for –fastp-5 and –fastp-3	int
Use this mean quality threshold for –fastp-5 and –fastp-3	int
Trim poly(G) tails (two-color sequencing artifacts) from the 3’ end	str
Minimum number of Gs to consider a poly(G) tail for –fastp-poly-g	int
Trim poly(X) tails (i.e. of any nucleotide) from the 3’ end	bool
Minimum number of bases to consider a poly(X) tail for –fastp-poly-x	int
Trim adapter sequences from the 3’ ends of reads	bool
Trim this adapter sequence from the 3’ ends of read 1s	str
Trim this adapter sequence from the 3’ ends of read 2s	str
Trim adapter sequences in this FASTA file from the 3’ ends of reads	str
Automatically detect the adapter sequences for paired-end reads	bool
Discard reads shorter than this length	int
Align reads in local mode rather than end-to-end mode	bool
Output paired-end reads whose mates align discordantly	bool
Attempt to align individual mates of pairs that fail to align	bool
Consider dovetailed mate pairs to align concordantly	bool
Consider nested mate pairs to align concordantly	bool
Discard alignments that score below this threshold	str
Discard paired-end alignments shorter than this many bases	int
Discard paired-end alignments longer than this many bases	int
Do not place gaps within this many bases from the end of a read	int
Use this seed length for Bowtie2	int
Seed Bowtie2 alignments at this interval	str
Discard alignments if over this many consecutive seed extensions fail	int
Re-seed reads with repetitive seeds up to this many times	int
Pad the alignment matrix with this many bases (to allow gaps)	int
Require paired mates to have this orientation	str
Output unaligned reads to a FASTQ file	bool
Discard reads with mapping qualities below this threshold	int
Separate each alignment map into forward- and reverse-strand reads	bool
With –sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded	bool
With –sep-strands, add this label to each reverse-strand reference	str
Discard alignment maps with fewer than this many reads	int
Number of reads in the FASTQ file(s)	int
Number of reads after trimming	int
Number of reads after alignment	dict[str, int]
Number of reads after filtering	dict[str, int]
Number of reads aligned to each reference	dict[str, int]
Checksum of the reference fasta (SHA-512)	str
Checksum(s) of the input fastq(s) (SHA-512)	dict[str, str]
Time began	str
Time ended	str
Time taken (minutes)	float
Version of SEISMIC-RNA	str

Align Reference Report: Example

{
    "Sample": "sample1",
    "Branches": {
        "align": ""
    },
    "Reference": "myref",
    "Seed for the random number generator": null,
    "Use demultiplexed mode": true,
    "Use paired-end mode": true,
    "Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files": 33,
    "Use fastp to QC, filter, and trim reads before alignment": true,
    "Trim low-quality bases from the 5' ends of reads": false,
    "Trim low-quality bases from the 3' ends of reads": true,
    "Use this window size (nt) for --fastp-5 and --fastp-3": 6,
    "Use this mean quality threshold for --fastp-5 and --fastp-3": 25,
    "Trim poly(G) tails (two-color sequencing artifacts) from the 3' end": "auto",
    "Minimum number of Gs to consider a poly(G) tail for --fastp-poly-g": 10,
    "Trim poly(X) tails (i.e. of any nucleotide) from the 3' end": false,
    "Minimum number of bases to consider a poly(X) tail for --fastp-poly-x": 10,
    "Trim adapter sequences from the 3' ends of reads": true,
    "Trim this adapter sequence from the 3' ends of read 1s": "",
    "Trim this adapter sequence from the 3' ends of read 2s": "",
    "Trim adapter sequences in this FASTA file from the 3' ends of reads": null,
    "Automatically detect the adapter sequences for paired-end reads": true,
    "Discard reads shorter than this length": 9,
    "Align reads in local mode rather than end-to-end mode": true,
    "Output paired-end reads whose mates align discordantly": false,
    "Attempt to align individual mates of pairs that fail to align": false,
    "Consider dovetailed mate pairs to align concordantly": false,
    "Consider nested mate pairs to align concordantly": true,
    "Discard alignments that score below this threshold": "L,1,0.8",
    "Discard paired-end alignments shorter than this many bases": 0,
    "Discard paired-end alignments longer than this many bases": 600,
    "Do not place gaps within this many bases from the end of a read": 4,
    "Use this seed length for Bowtie2": 20,
    "Seed Bowtie2 alignments at this interval": "L,1,0.1",
    "Discard alignments if over this many consecutive seed extensions fail": 4,
    "Re-seed reads with repetitive seeds up to this many times": 2,
    "Pad the alignment matrix with this many bases (to allow gaps)": 2,
    "Require paired mates to have this orientation": "fr",
    "Output unaligned reads to a FASTQ file": true,
    "Discard reads with mapping qualities below this threshold": 25,
    "Separate each alignment map into forward- and reverse-strand reads": false,
    "With --sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded": false,
    "With --sep-strands, add this label to each reverse-strand reference": "-rev",
    "Discard alignment maps with fewer than this many reads": 1000,
    "Number of reads in the FASTQ file(s)": 4008,
    "Number of reads after trimming": 4008,
    "Number of reads after alignment": {
        "reads, were paired": 4008,
        "reads, were paired, aligned concordantly 0 times": 372,
        "reads, were paired, aligned concordantly exactly 1 time": 3636,
        "reads, were paired, aligned concordantly >1 times": 0
    },
    "Number of reads after filtering": {
        "paired-end, both mates mapped": 3595,
        "paired-end, one mate unmapped": 0
    },
    "Number of reads aligned to each reference": {
        "myref": 3595
    },
    "Checksum of the reference fasta (SHA-512)": "e4dcaae215ebadadc57010d22d93f4311cdc0bc02fc2f65db558a14b671d898ef8ff541817bf374aa60688627dbb9601581f7b271e60eb80cc36fc0c7dd51882",
    "Checksum(s) of the input fastq(s) (SHA-512)": {
        "fastq1": "a28f7d8cf7856603cee938c0d6a91561063d6eb8a34ebc2d9bee2b9fa8c04f9c528afe8e6b039bb62467bf71a6358d892fc5fdd2bec9e51902a116f67b791a9d",
        "fastq2": "15242a00abef156c10b18bef6717cd2e9b1ee54165d89aa490ea0176e7977d7f24a3c9e12dece493c67a6ab77b9a43f7ad291a60189275266d22a31882ef1046"
    },
    "Time began": "2026-05-31 at 12:53:08",
    "Time ended": "2026-05-31 at 12:53:09",
    "Time taken (minutes)": 0.01,
    "Version of SEISMIC-RNA": "0.25.3"
}