Description

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

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

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘test_ref’]

reference{:bash}

:file

Reference database in FASTA format.

bam_format{:bash}

:boolean

Specify that output should be in BAM format

bam_index_extension{:bash}

:string

BAM alignment index extension (e.g. “bai”)

cigar_paf_format{:bash}

:boolean

Specify that output CIGAR should be in PAF format

cigar_bam{:bash}

: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

paf{:bash}

meta{:bash}

:map

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

*.paf{:bash}

:file

Alignment in PAF format

*.paf

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Alignment in BAM format

*.bam

index{:bash}

meta{:bash}

:map

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

*.bam.${bam_index_extension}{:bash}

:file

BAM alignment index

*.bam.*

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

minimap2
MIT

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

github.com/lh3/minimap2 github.com/lh3/minimap2#uguide
included in
abotyperbacasscircdnacrisprseqevexplorergenomeassemblerisoseqmagmethylongradseqscnanoseqtaxprofilerviralmetagenome
maintainers
Github user heuermh
Github user sofstam
Github user sateeshperi
Github user jfy133
Github user fellen31
get in touch
Ask a question on Slack Open an issue on GitHub