checkm_lineagewf

Tags: quality-control completeness contamination marker-genes lineage bacteria archaea sample-scope

Assess genome quality using lineage-specific marker sets.

Uses CheckM to estimate the completeness and contamination of genome assemblies. It places the genome into a reference tree to select an appropriate set of single-copy marker genes, then calculates quality metrics based on the recovery of these markers.

Database Required

Requires the CheckM reference database (~275GB uncompressed) to be configured via the CHECKM_DATA_PATH environment variable or pre-installed in the container.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited genome quality report with completeness and contamination estimates
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

CheckM Parameters

Parameter	Type	Default	Description
--checkm_unique	integer	10	Minimum number of unique phylogenetic markers required to use lineage-specific marker set.
--checkm_multi	integer	10	Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set.
--checkm_aai_strain	number	0.9	AAI threshold used to identify strain heterogeneity
--checkm_length	number	0.7	Percent overlap between target and query

Used By

Subworkflows

• checkm - Assess metagenome bin completeness using CheckM.

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)

• pplacer
  Matsen FA, Kodner RB, Armbrust EV pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11, 538 (2010)

Source

View source on GitHub

Version

CHECKM_LINEAGEWF:
    - checkm-genome: 1.2.5