quast

Tags: quast assembly quality-control n50 metrics sample-scope

Quality Assessment Tool for Genome Assemblies.

Uses QUAST to evaluate genome assemblies by computing various metrics such as N50, gene counts, and assembly length.

Inputs

record (
    meta: Record,
    fna: Path,
    tsv_meta: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format
tsv_meta	Path	Meta file containing reference size information

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	Transposed report in TSV format
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

Quast Parameters

Parameter	Type	Default	Description
--quast_contig_thresholds	string	0,1000,10000,100000,250000,1000000	Comma-separated list of contig length thresholds

Used By

Subworkflows

• quast - Evaluate assembly quality using QUAST.

Workflows

• quast - Quality assessment of assembled contigs using QUAST.

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)

• QUAST
  Gurevich A, Saveliev V, Vyahhi N, Tesler G QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075 (2013)

Source

View source on GitHub

Version

QUAST:
    - quast: 5.3.0