minimap2_align
Description¶
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Keywords: align, fasta, fastq, genome, paf, reference
Installation¶
ebi-metagenomics/minimap2/align
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install minimap2/align
Tools¶
minimap2¶
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:false ] | - |
reads |
file | List of input FASTA or FASTQ files of size 1 and 2 for single-end and paired-end data, respectively. | - |
meta2 |
map | Groovy Map containing reference information e.g. [ id:'test_ref'] | - |
reference |
file | Reference database in FASTA format. | - |
bam_format |
boolean | Specify that output should be in BAM format | - |
bam_index_extension |
string | BAM alignment index extension (e.g. "bai") | - |
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 |
|---|---|---|---|
paf |
file | - | |
bam |
file | - | |
index |
file | - | |
versions |
file | - |
People¶
Authors¶
Maintainers