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.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--reference -i --input | file required | Reference fasta or .mmi index. |
--query -q | file required | Query sequences (FASTQ/FASTA). |
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. |
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. |
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 Relationships
Used by
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No components use this component.
Current component
minimap2/minimap2_alignbiobox v0.5.0
Uses
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