checkm
Tags: metagenome bin completeness contamination mag quality sample-scope
Assess metagenome bin completeness using CheckM.
This subworkflow evaluates the quality and completeness of metagenome-assembled genomes (MAGs) using CheckM. It provides a comprehensive assessment based on lineage-specific marker sets, estimating completeness and contamination of genome bins. The workflow generates detailed reports including marker gene statistics, taxonomy predictions, and quality metrics for each bin.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Metagenome-assembled genome bins to evaluate. Each record contains metadata |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | Tab-delimited CheckM quality assessment results |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- checkm_lineagewf - Assess genome quality using lineage-specific marker sets.
Used By
This subworkflow is used by the following workflows:
- checkm - Assessment of microbial genome assembly quality.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
CheckM
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043-1055 (2015)