tblastx

Tags: fasta blast alignment protein translation bactopia-tool

Search against translated nucleotide databases using translated nucleotide queries.

This Bactopia Tool uses TBLASTX to query translated nucleotide sequences against translated nucleotide databases for comprehensive homology search at the protein level.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── tblastx-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.tblastx.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── tblastx-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── tblastx-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── tblastx.tsv
        └── nf-reports
            ├── tblastx-dag.dot
            ├── tblastx-report.html
            └── tblastx-timeline.html

Per-Sample Results

File	Description
*.tblastx.tsv	TBLASTX alignment results in tabular format
*.tblastx.html	Interactive HTML report of TBLASTX results

Merged Results

File	Description
tblastx.tsv	Merged TBLASTX results 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
tblastx-dag.dot	The Nextflow DAG visualization
tblastx-report.html	The Nextflow Execution Report
tblastx-timeline.html	The Nextflow Timeline Report
tblastx-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

TBLASTX Parameters

Parameter	Type	Default	Description
--tblastx_query	string		A fasta file containing the query sequences to BLAST against the database
--tblastx_outfmt	string	sseqid qseqid pident qlen slen length nident positive mismatch gapopen gaps qstart qend sstart send evalue bitscore	The columns to include with -outfmt 6
--tblastx_opts	string		Additional options to pass to BLASTN
--tblastx_qcov_hsp_perc	integer	50	Percent query coverage per hsp
--tblastx_max_target_seqs	integer	2000	Maximum number of aligned sequences to keep

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:

• tblastx - Translate nucleotide query sequences and search nucleotide database.

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)

• BLAST
  Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009)

Source

View source on GitHub