minimap2/minimap2_align

Alignment

Mapper

Minimap2

Description

A versatile pairwise aligner for genomic and spliced nucleotide sequences.
This component maps DNA or mRNA query sequences against a reference database (FASTA or .mmi index).
By default, it outputs mapping coordinates in PAF format. If the --bam flag is provided, it outputs a sorted and indexed BAM file.

Type

bash_script

License

MIT

Keywords

Alignment

Mapper

Minimap2

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.paf"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/minimap2/minimap2_align/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--reference -i --input	file required	Reference fasta or .mmi index.
--query -q	file required	Query sequences (FASTQ/FASTA).

Name

Type & Properties

--reference

-i

--input

file

required

--query

-q

file

required

Options

Name	Type & Properties	Description
--preset -x	string	Preset alignment options (e.g. map-ont, map-hifi, map-pb, asm5, asm10, asm20, splice, sr, ava-ont, ava-pb). Run `minimap2 -x` for the full list.

Name

Type & Properties

--preset

-x

string

Outputs

Name	Type & Properties	Description
--bam	boolean_true	Output BAM instead of PAF.
--cigar_paf	boolean_true	Output CIGAR in PAF format (-c flag).
--cigar_bam	boolean_true	Write long CIGARs in BAM CG tag (-L flag).
--output -o	file required output	Output alignment file in PAF (default) or BAM format.

Name

Type & Properties

--bam

boolean_true

--cigar_paf

boolean_true

--cigar_bam

boolean_true

--output

-o

file

required

output