GENOMESCOPE

Reference-free profiling of polyploid genomes

URL: https://github.com/tbenavi1/genomescope2.0

Example

This wrapper can be used in the following way:

rule genomescope:
    input:
        hist="{sample}.hist",
    output:
        multiext(
            "{sample}/",
            "linear_plot.png",
            "log_plot.png",
            "model.txt",
            "progress.txt",
            "SIMULATED_testing.tsv",
            "summary.txt",
            "transformed_linear_plot.png",
            "transformed_log_plot.png",
        ),
    log:
        "logs/genomescope/{sample}.log",
    params:
        extra="--kmer_length 32 --testing",
    wrapper:
        "v1.14.1-1-gad41354/bio/genomescope"

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

  • The extra param allows for additional program arguments (kmer length -k/–kmer_length is mandatory).

Software dependencies

  • genomescope2=2.0

Input/Output

Input:

  • kmer histogram

Output:

  • inferred genome characteristics and plots

Authors

  • Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__license__ = "MIT"


import os
from snakemake.shell import shell


extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)


out_basename = os.path.commonpath(snakemake.output)


shell("genomescope2 --input {snakemake.input} {extra} --output {out_basename} {log}")