scrubber

Tags: metagenomics decontamination human-removal read-filtering bactopia-tool

Removal of human and contaminant sequences from metagenomic reads.

This Bactopia Tool removes human and other contaminant sequences from metagenomic reads using either SRA Human Scrubber or nohuman with the HPRC human database. The tool provides flexible contamination removal with detailed reporting of read classification and filtering statistics. It processes paired-end or single-end reads, producing cleaned FASTQ files with human sequences removed and comprehensive reports documenting the decontamination process.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── nohuman
│           ├── <SAMPLE_NAME>.scrub.report.tsv
│           ├── <SAMPLE_NAME>_R1.scrubbed.fastq.gz
│           ├── <SAMPLE_NAME>_R2.scrubbed.fastq.gz
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── scrubber-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── scrubber-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── scrubber.tsv
        └── nf-reports
            ├── scrubber-dag.dot
            ├── scrubber-report.html
            └── scrubber-timeline.html

Per-Sample Results

File	Description
*.scrubbed.fastq.gz	Cleaned reads after human sequence removal
*.scrub.report.tsv	Report of read classification and removal statistics

Merged Results

File	Description
scrubber.tsv	Merged TSV file containing scrubber 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
scrubber-dag.dot	The Nextflow DAG visualization
scrubber-report.html	The Nextflow Execution Report
scrubber-timeline.html	The Nextflow Timeline Report
scrubber-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

SRA Human Scrubber Parameters

Parameter	Type	Default	Description
--use_srascrubber	boolean	false	Use SRAHumanScrubber for scrubbing human reads

Nohuman Download Parameters

Parameter	Type	Default	Description
--nohuman_db	string		Path to the nohuman database or directory to download it to
--nohuman_db_version	string		Database version to download (default: latest HPRC release)
--nohuman_save_as_tarball	boolean	false	Save the nohuman database as a tarball
--download_nohuman	boolean	false	Download the nohuman database to the path given by --nohuman_db

Nohuman Run Parameters

Parameter	Type	Default	Description
--nohuman_db	string		Path to the nohuman database directory or tarball
--nohuman_confidence	number	0.0	Kraken2 minimum confidence score for classification (0.0-1.0)
--nohuman_human	boolean	false	Invert output to keep only human reads instead of removing them
--nohuman_save_report	boolean	false	Save the Kraken2 classification report

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:

• scrubber - Remove contaminant sequences from metagenomic data.

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)

• Kraken2
  Wood DE, Lu J, Langmead B Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. (2019)

• SRA Human Scrubber
  Katz KS, Shutov O, Lapoint R, Kimelman M, Brister JR, and O'Sullivan C STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. Genome Biology, 22(1), 270 (2021)

Source

View source on GitHub