busco

Deprecated. Use aweMAGs instead.

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metashot/busco is a pipeline for assessing the quality of prokaryotic and eukaryotic genomes using BUSCO.

Note: This workflow is not intended for classify "finished" genomes. The "finished" category is reserved for genomes that can be assembled with extensive manual review and editing.

• MetaShot Home

Main features

• Input: genomes in FASTA format;
• Basic assembly statistics using BBTools;
• Assessing genome completeness and contamination using BUSCO v4.

Quick start

1. Install Docker (or Singulariry) and Nextflow (see Dependencies);
2. Start running the analysis:

nextflow run metashot/busco \
  --genomes '*.fa' \
  --outdir results

Parameters

Parameters are decladed in nextflow.config.

Parameter	Default	Description
genomes	"data/*.fa"	input genomes in FASTA format
outdir	results	output directory
busco_db	none	BUSCO download folder for offline mode (see https://busco.ezlab.org/busco_userguide.html#offline)
lineage	auto	lineage. It can be auto, auto-prok, auto-euk, a dataset name (e.g bacteria or bacteria_odb10) or a path (e.g. /home/user/bacteria_odb10)
min_completeness	50	discard sequences with less than 50% completeness
max_contamination	10	discard sequences with more than 10% contamination

Resource limits

Parameter	Default	Description
max_cpus	8	maximum number of CPUs for each process
max_memory	32.GB	maximum memory for each process
max_time	24.h	maximum time for each process

See also System requirements.

Output

The files and directories listed below will be created in the results directory after the pipeline has finished.

Main outputs

• genome_info.tsv: summary of genomes quality (including completeness, contamination, N50, BUSCO counts...) in tab-separated format.
• filtered: genomes filtered by the --min_completeness and --max_contamination options;

Secondary outputs

• busco: contains the BUSCO short summaries and logs for each input genome;
• statswrapper: contains the original statistics file created by the BBTools statswrapper.sh command.

Documetation

Completeness and contamination

Completeness is defined as as 100 minus the fraction of missing BUSCOs and contamination as the fraction of duplicated BUSCOs:

completeness % = 100 x (1 - Missing / Total)

contamination % = 100 x Duplicated / Complete

Reproducibility

See Reproducibility.

Credits

See Credits.