Description

Calculate read coverage per-genome

Input

Name
Description
Pattern

0 ()

1 ()

0 ()

1 ()

bam_input (boolean)

True if input is bam files

interleaved (boolean)

True if input is interleaved fastq file

ref_mode (string)

How to interpret the reference input:

  • "dir": Treat as a directory containing one or more FASTA files.
  • "file": Treat as a single FASTA file.
  • "auto": Automatically detect based on whether the reference path is a directory or file. Defaults to "auto" if not provided.
^(dir|file|auto)$

enable_bam_output (boolean)

True to enable BAM output of aligned reads

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

Tools

coverm Documentation

CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications

https://github.com/wwood/CoverMdoi: 10.5281/zenodo.10531253License: GPL v3
nf-core pipelines with this module
metagenomeassembly
Authors