ariba

Tags: fastq assembly resistance virulence gene-detection bactopia-tool

Gene identification through local assemblies.

This Bactopia Tool uses ARIBA to rapidly identify genes in a database by creating local assemblies from short-read data. ARIBA performs reference-based assembly and variant calling for gene detection.

Usage

Bactopia CLI:

bactopia --wf ariba \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/ariba/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── ariba
│           └── card
│               ├── <SAMPLE_NAME>-report.tsv
│               ├── <SAMPLE_NAME>-summary.csv
│               ├── logs
│               │   └── card
│               │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│               │       └── versions.yml
│               └── supplemental
│                   ├── assembled_genes.fa.gz
│                   ├── assembled_seqs.fa.gz
│                   ├── assemblies.fa.gz
│                   ├── debug.report.tsv
│                   ├── log.clusters.gz
│                   └── version_info.txt
└── bactopia-runs
    └── ariba-card-<TIMESTAMP>
        ├── merged-results
        │   ├── card-report.tsv
        │   ├── card-summary.csv
        │   └── logs
        │       ├── card-report-concat
        │       │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │       │   └── versions.yml
        │       └── card-summary-concat
        │           ├── nf.command.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── ariba-dag.dot
            ├── ariba-report.html
            └── ariba-timeline.html

Per-Sample Results

File	Description
*-report.tsv	Gene detection report for each sample
*-summary.csv	Summary of gene detection results
assembled_genes.fa.gz	Assembled genes in compressed FASTA format
assembled_seqs.fa.gz	Assembled sequences matching references
assemblies.fa.gz	Raw local assemblies
debug.report.tsv	Detailed report including synonymous mutations
log.clusters.gz	Analysis log file
version_info.txt	Version information for ARIBA and dependencies

Merged Results

File	Description
ariba-report.tsv	Merged gene detection reports from all samples
ariba-summary.csv	Merged summary reports from all samples

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
ariba-dag.dot	The Nextflow DAG visualization
ariba-report.html	The Nextflow Execution Report
ariba-timeline.html	The Nextflow Timeline Report
ariba-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

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

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

Ariba Run Parameters

Parameter	Type	Default	Description
--ariba_db	string		A database to query, if unavailable it will be downloaded to the path given by --datasets_cache (choices: argannot, card, ncbi, megares, plasmidfinder, resfinder, srst2_argannot, vfdb_core, vfdb_full, virulencefinder)
--ariba_nucmer_min_id	integer	90	Minimum alignment identity (delta-filter -i)
--ariba_nucmer_min_len	integer	20	Minimum alignment identity (delta-filter -i)
--ariba_assembly_cov	integer	50	Target read coverage when sampling reads for assembly

Filtering Parameters

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

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

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--wf	string	bactopia	Specify which workflow or Bactopia Tool to execute
--list_wfs	boolean		List the available workflows and Bactopia Tools to use with '--wf'
--help_all	boolean		An alias for --help --show_hidden_params
--version	boolean		Display version text.

Composition

This workflow uses the following subworkflows:

• ariba - Rapidly identify genes by creating local assemblies from paired-end reads.

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)

• Ariba
  Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 3, e000131 (2017)

Source

View source on GitHub