Description

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input FASTA or FASTQ files of size 1 and 2 for single-end
and paired-end data, respectively.

reference (file)

Reference database in FASTA format.

bam_format (boolean)

Specify that output should be in BAM format

cigar_paf_format (boolean)

Specify that output CIGAR should be in PAF format

cigar_bam (boolean)

Write CIGAR with >65535 ops at the CG tag. This is recommended when
doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

paf (file)

Alignment in PAF format

*.paf

bam (file)

Alignment in BAM format

*.bam

versions (file)

File containing software versions

versions.yml
included in
circdna crisprseq isoseq radseq taxprofiler
authors
Github user heuermh Github user sofstam Github user sateeshperi Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

minimap2
MIT

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

github.com/lh3/minimap2 github.com/lh3/minimap2#uguide