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.

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── busco
│           └── <BUSCO_LINEAGE>
│               ├── <SAMPLE_NAME>-summary.txt
│               ├── logs
│               │   ├── bbtools_{err|out}.log
│               │   ├── busco.log
│               │   ├── hmmsearch_{err|out}.log
│               │   ├── nf-busco.{begin,err,log,out,run,sh,trace}
│               │   ├── prodigal_{err|out}.log
│               │   ├── prodigal_mode_single_code_#_{err,out}.log
│               │   └── versions.yml
│               ├── prodigal_output
│               │   └── predicted_genes
│               │       ├── predicted.{faa,fna}
│               │       └── tmp
│               │           └── prodigal_mode_single_code_#.{faa,fna}
│               ├── run_<BUSCO_LINEAGE>
│               │   ├── busco_sequences
│               │   │   ├── fragmented_busco_sequences
│               │   │   │   └── <ID>.{faa,fna
│               │   │   ├── multi_copy_busco_sequences
│               │   │   └── single_copy_busco_sequences
│               │   │       └── <ID>.{faa,fna}
│               │   ├── full_table.tsv
│               │   ├── hmmer_output
│               │   │   └── <ID>.out
│               │   ├── missing_busco_list.tsv
│               │   └── short_summary.{json|txt}
│               └── short_summary.specific.bacteria_odb10.GCF_000292685.fna.{json|txt}
└── bactopia-runs
    └── busco-<TIMESTAMP>
        ├── merged-results
        │   ├── busco.tsv
        │   └── logs
        │       └── busco-concat
        │           ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── busco-dag.dot
            ├── busco-report.html
            ├── busco-timeline.html
            └── busco-trace.txt

Results¶

Merged Results¶

Below are results that are concatenated into a single file.

Filename	Description

busco¶

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

Filename	Description
<SAMPLE_NAME>-summary.txt	A summary of the BUSCO results
prodigal_output	Below are the outputs from the Prodigal gene-prediction step.
run_<BUSCO_LINEAGE>/busco_sequences	FASTA format file for each BUSCO gene identified
run_<BUSCO_LINEAGE>/full_table.tsv	Complete results in a tab-delimited format with scores and lengths of BUSCO matches
run_<BUSCO_LINEAGE>/hmmer_output	Tab-delimited output from HMMER
run_<BUSCO_LINEAGE>/missing_busco_list.tsv	Tab-delimited list of missing BUSCOs
run_<BUSCO_LINEAGE>/short_summary.json	A summary of BUSCO matches in JSON format
run_<BUSCO_LINEAGE>/short_summary.txt	A summary of BUSCO matches
short_summary.specific.<BUSCO_LINEAGE>.<SAMPLE_NAME>.json	A summary of BUSCO matches in JSON format per-sample
short_summary.specific.<BUSCO_LINEAGE>.<SAMPLE_NAME>.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 folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.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
`--bactopia`	The path to bactopia results to use as inputs Type: `string`

Filtering Parameters¶

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

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

BUSCO Parameters¶

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

Optional Parameters¶

These optional parameters can be useful in certain settings.

Parameter	Description
`--outdir`	Base directory to write results to Type: `string`, Default: `./`
`--run_name`	Name of the directory to hold results Type: `string`, Default: `bactopia`
`--skip_compression`	Ouput files will not be compressed Type: `boolean`
`--datasets`	The path to cache datasets to Type: `string`
`--keep_all_files`	Keeps all analysis files created Type: `boolean`

Max Job Request Parameters¶

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

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

Nextflow Configuration Parameters¶

Parameters to fine-tune your Nextflow setup.

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

Nextflow Profile Parameters¶