Description

Aligns a subset of sequencing reads from a FASTx file to a reference genome using minimap2. Can either output the alignment in PAF format, or alternatively will pipe the resulting alignments through samtools view and samtools sort, outputting an alignment in BAM format.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

fastx (file)

FASTx file of reads to map a chunk of

*.{fasta,fa,fasta.gz,fa.gz,fq,fq.gz}

fxi (file)

FXI index file of the input created by pyfastx

*.fxi

pg_lines (string)

Optional program lines from CRAM header to handle @PG deduplication

meta2 (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

index (file)

minimap2 index of the reference to be aligned to

reference (file)

FASTA file or minimap2 index of the reference to be aligned to

chunkn (integer)

Integer index of FASTA chunk to map

range (list)

Start and end indices defining FASTA slices to align, 0-indexed

bam_format (boolean)

Output PAF format or BAM format alignments

Output

Name
Description
Pattern

bam

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.bam (file)

BAM file of mapped sequences

*.bam

paf

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.paf.gz (file)

bgzipped PAF file of mapped sequences

*.paf.gz

versions_minimap2

${task.process} (string)

The name of the process

minimap2 (string)

The name of the tool

minimap2 --version | sed "s/minimap2 //g" (eval)

The expression to obtain the version of the tool

versions_samtools

${task.process} (string)

The name of the process

samtools (string)

The name of the tool

samtools version | sed "1!d;s/.* //" (eval)

The expression to obtain the version of the tool

versions_slice_fasta

${task.process} (string)

The name of the process

slice_fasta.py (string)

The name of the tool

slice_fasta.py --version (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

slice_fasta.py (string)

The name of the tool

slice_fasta.py --version (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

samtools (string)

The name of the tool

samtools version | sed "1!d;s/.* //" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

minimap2 (string)

The name of the tool

minimap2 --version | sed "s/minimap2 //g" (eval)

The expression to obtain the version of the tool

Tools

pyfastx Documentation

The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number.

License: MIT

samtools Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT

minimap2 Documentation

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

License: MIT
Pipelines with this module
asccgenomeassemblymetagenomeassembly
Authors