Description

Digest concatemer reads into monomers at restriction enzyme recognition sites. Reads FASTQ/FASTA (optionally gzipped), BAM, or CRAM and writes gzipped FASTQ monomers ready for alignment. BAM/CRAM are converted with samtools fastq (reference FASTA required for CRAM). Optional digest_reads.py arguments such as --min-len can be passed via task.ext.args.

Input

Name
Description
Pattern

meta (map)

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

reads (file)

Concatemer reads as FASTQ/FASTA (optionally gzipped), BAM, or CRAM. BAM/CRAM are converted with samtools fastq before digestion. Pass a single file or a list of files of the same type per sample; multiple BAM/CRAM files are streamed together, and multiple FASTQ/FASTA files are concatenated before digestion.

*.{bam,cram,fq,fastq,fa,fasta,fq.gz,fastq.gz,fa.gz,fasta.gz}

reference (file)

Reference assembly FASTA. Required for CRAM; pass assembly FASTA for all input types.

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

cutter (string)

Restriction enzyme name (e.g. NlaIII, DpnII, HindIII) or recognition sequence (e.g. CATG)

Output

Name
Description
Pattern

digested_reads

meta (map)

Groovy Map containing sample information

*.fastq.gz (file)

Gzipped FASTQ digested monomer reads

*.fastq.gz

versions_python

${task.process} (string)

The process the versions were collected from

python (string)

The tool name

python -c "import sys; print(sys.version.split()[0])" (eval)

The expression to obtain the version of the tool

versions_samtools

${task.process} (string)

The process the versions were collected from

samtools (string)

The tool name

samtools --version | head -n1 | sed "s/ /,/" (eval)

The expression to obtain the version of the tool

versions_digest_reads

${task.process} (string)

The process the versions were collected from

digest_reads.py (string)

The tool name

digest_reads.py --version | sed 's/^.* //' (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

python (string)

The tool name

python -c "import sys; print(sys.version.split()[0])" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The process the versions were collected from

digest_reads.py (string)

The tool name

digest_reads.py --version | sed 's/^.* //' (eval)

The expression to obtain the version of the tool

${task.process} (string)

The process the versions were collected from

samtools (string)

The tool name

samtools --version | head -n1 | sed "s/ /,/" (eval)

The expression to obtain the version of the tool

Tools

digest_reads.py Documentation

Split concatemer read sequences at restriction enzyme cut sites and emit monomer reads as FASTQ.

License: MIT

samtools Documentation

Convert BAM/CRAM alignments to FASTQ before digestion

License: MIT

python Documentation

Python runtime for digest_reads.py

License: PSF-2.0
Authors