SEQTK MERGEPE

Interleave two paired-end FASTA/Q files

URL: https://github.com/lh3/seqtk

Example

This wrapper can be used in the following way:

rule seqtk_mergepe:
    input:
        r1="{sample}.1.fastq.gz",
        r2="{sample}.2.fastq.gz",
    output:
        merged="{sample}.merged.fastq.gz",
    params:
        compress_lvl=9,
    log:
        "logs/seqtk_mergepe/{sample}.log",
    threads: 2
    wrapper:
        "v2.0.0/bio/seqtk/mergepe"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Notes

Multiple threads can be used during compression of the output file with pigz.

Software dependencies

• seqtk=1.3
• pigz=2.6

Input/Output

Input:

• paired fastq files - can be compressed in gzip format (*.gz).

Output:

• a single, interleaved FASTA/Q file. By default, the output will be compressed, use the param compress_lvl to change this.

Params

• compress_lvl: Regulate the speed of compression using the specified digit, where 1 indicates the fastest compression method (less compression) and 9 indicates the slowest compression method (best compression). 0 is no compression. 11 gives a few percent better compression at a severe cost in execution time, using the zopfli algorithm. The default is 6.

Authors

• Michael Hall

Code

"""Snakemake wrapper for interleaving reads from paired FASTA/Q files using seqtk."""

__author__ = "Michael Hall"
__copyright__ = "Copyright 2021, Michael Hall"
__email__ = "michael@mbh.sh"
__license__ = "MIT"

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True, append=False)
compress_lvl = int(snakemake.params.get("compress_lvl", 6))

shell(
    "(seqtk mergepe {snakemake.input} "
    "| pigz -{compress_lvl} -c -p {snakemake.threads}) > {snakemake.output} {log}"
)