Bactopia Tool - busco

The busco module uses BUSCO (or Benchmarking Universal Single-Copy Orthologs) to assess the completeness of your assembly.

Example Usage

bactopia --wf busco \
  --bactopia /path/to/your/bactopia/results \ 
  --include includes.txt  

Output Overview

Below is the default output structure for the busco tool. Where possible the file descriptions below were modified from a tools description.

busco/
├── <LINEAGE>
│   ├── <SAMPLE_NAME>
│   │   ├── logs/
│   │   ├── prodigal_output/
│   │   ├── run_<LINEAGE>/
│   │   │   ├── busco_sequences
│   │   │   ├── full_table.tsv
│   │   │   ├── hmmer_output/
│   │   │   ├── missing_busco_list.tsv
│   │   │   ├── short_summary.json
│   │   │   └── short_summary.txt
│   │   ├── short_summary.specific.<LINEAGE>.<SAMPLE_NAME>.json
│   │   └── short_summary.specific.<LINEAGE>.<SAMPLE_NAME>.txt
│   ├── <LINEAGE>-summary.txt
│   └── logs
│       └── busco.log
├── logs
│   ├── busco
│   │   └── <LINEAGE>
│   │       ├── nf-busco.{begin,err,log,out,run,sh,trace}
│   │       └── versions.yml
│   ├── csvtk_concat
│   │   ├── nf-csvtk_concat.{begin,err,log,out,run,sh,trace}
│   │   └── versions.yml
│   └── custom_dumpsoftwareversions
│       ├── nf-custom_dumpsoftwareversions.{begin,err,log,out,run,sh,trace}
│       └── versions.yml
├── nf-reports
│   ├── busco-dag.dot
│   ├── busco-report.html
│   ├── busco-timeline.html
│   └── busco-trace.txt
├── busco.tsv
├── software_versions.yml
└── software_versions_mqc.yml

Results

Top Level

Below are results that are in the base directory.

Filename	Description
busco.tsv	A merged TSV of all lineages used by BUSCO

busco

Below is a description of the per-lineage results from BUSCO.

Filename/Folder	Description
/-summary.txt	Tab-delimited lineage results for all samples
/logs/busco.log	Detailed information about the BUSCO run
//logs/	Log files for individual tools per-sample
//prodigal_output/	Outputs from the Prodigal gene-prediction step
//run_/busco_sequences	FASTA format file for each BUSCO gene identified
//run_/full_table.tsv	Complete results in a tab-delimited format with scores and lengths of BUSCO matches
//run_/hmmer_output	Tab-delimited output from HMMER
//run_/missing_busco_list.tsv	Tab-delimited list of missing BUSCOs
//run_/short_summary.json	A summary of BUSCO matches in JSON format
//run_/short_summary.txt	A summary of BUSCO matches
//short_summary.specific...json	A summary of BUSCO matches in JSON format per-sample
//short_summary.specific...txt	A summary of BUSCO matches per-sample

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a logs folder containing helpful files for you to review if the need ever arises.

Filename	Description
nf-<PROCESS_NAME>.begin	An empty file used to designate the process started
nf-<PROCESS_NAME>.err	Contains STDERR outputs from the process
nf-<PROCESS_NAME>.log	Contains both STDERR and STDOUT outputs from the process
nf-<PROCESS_NAME>.out	Contains STDOUT outputs from the process
nf-<PROCESS_NAME>.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
nf-<PROCESS_NAME>.sh	The script executed by bash for the process
nf-<PROCESS_NAME>.trace	The Nextflow Trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
busco-dag.dot	The Nextflow DAG visualisation
busco-report.html	The Nextflow Execution Report
busco-timeline.html	The Nextflow Timeline Report
busco-trace.txt	The Nextflow Trace report

Program Versions

At the end of each run, each of the versions.yml files are merged into the files below.

Filename	Description
software_versions.yml	A complete list of programs and versions used by each process
software_versions_mqc.yml	A complete list of programs and versions formatted for MultiQC

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Description	Default
--bactopia	The path to bactopia results to use as inputs

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Description	Default
--include	A text file containing sample names (one per line) to include from the analysis
--exclude	A text file containing sample names (one per line) to exclude from the analysis

BUSCO Parameters

Parameter	Description	Default
--busco_lineage	Specify the name of the BUSCO lineage to be used (can separate by comma)	bacteria_odb10
--busco_evalue	E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03	1e-03
--busco_limit	Total candidate regions to consider per BUSCO	3
--metaeuk_parameters	Additional Metaeuk first-pass arguments contained within a single pair of quotation marks, separated by commas
--metaeuk_rerun_parameters	Additional Metaeuk second-pass arguments contained within a single pair of quotation marks, separated by commas
--use_augustus	Use augustus gene predictor for eukaryote runs	False
--augustus_parameters	Additional Augustus arguments contained within a single pair of quotation marks, separated by commas
--augustus_species	Specify a species for Augustus training
--augustus_long	Optimization Augustus self-training mode	False

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Description	Default
--outdir	Base directory to write results to	./
--run_name	Name of the directory to hold results	bactopia
--skip_compression	Ouput files will not be compressed	False
--keep_all_files	Keeps all analysis files created	False

Max Job Request Parameters

Set the top limit for requested resources for any single job.

Parameter	Description	Default
--max_retry	Maximum times to retry a process before allowing it to fail.	3
--max_cpus	Maximum number of CPUs that can be requested for any single job.	4
--max_memory	Maximum amount of memory (in GB) that can be requested for any single job.	32
--max_time	Maximum amount of time (in minutes) that can be requested for any single job.	120
--max_downloads	Maximum number of samples to download at a time	3

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Description	Default
--nfconfig	A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_mode	Method used to save pipeline results to output directory.	copy
--infodir	Directory to keep pipeline Nextflow logs and reports.	${params.outdir}/pipeline_info
--force	Nextflow will overwrite existing output files.	False
--cleanup_workdir	After Bactopia is successfully executed, the work directory will be deleted.	False

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Description	Default
--condadir	Directory to Nextflow should use for Conda environments
--registry	Docker registry to pull containers from.	dockerhub
--singularity_cache	Directory where remote Singularity images are stored.
--singularity_pull_docker_container	Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuild	Force overwrite of existing pre-built environments.	False
--queue	Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)	general,high-memory
--cluster_opts	Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--disable_scratch	All intermediate files created on worker nodes of will be transferred to the head node.	False

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Description	Default
--monochrome_logs	Do not use coloured log outputs.
--nfdir	Print directory Nextflow has pulled Bactopia to
--sleep_time	The amount of time (seconds) Nextflow will wait after setting up datasets before execution.	5
--validate_params	Boolean whether to validate parameters against the schema at runtime	True
--help	Display help text.
--wf	Specify which workflow or Bactopia Tool to execute	bactopia
--list_wfs	List the available workflows and Bactopia Tools to use with '--wf'
--show_hidden_params	Show all params when using --help
--help_all	An alias for --help --show_hidden_params
--version	Display version text.

Citations

If you use Bactopia and busco 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)

• BUSCO
  Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution 38(10), 4647–4654. (2021)