Rust-Bio-Tools

A set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio. Rust-Bio-Tools provides a command rbt, which currently supports the following operations:

• a linear time implementation for fuzzy matching of two vcf/bcf files (rbt vcf-match)
• a vcf/bcf to txt converter, that flexibly allows to select tags and properly handles multiallelic sites (rbt vcf-to-txt)
• a linear time round-robin FASTQ splitter that splits a given FASTQ files into a given number of chunks (rbt fastq-split)
• a linear time extraction of depth information from BAMs at given loci (rbt bam-depth)
• a utility to quickly filter records from a FASTQ file (rbt fastq-filter)
• a tool to merge BAM or FASTQ reads using marked duplicates respectively unique molecular identifiers (UMIs) (rbt collapse-reads-to-fragments bam|fastq)
• a tool to generate interactive HTML based reports that offer multiple plots visualizing the provided genomics data in VCF and BAM format (rbt vcf-report)
• a tool to generate an interactive HTML based report from a csv file including visualizations (rbt csv-report)
• a tool for splitting VCF/BCF files into N equal chunks, including BND support (rbt vcf-split)
• a tool to generate visualizations for a specific region of one or multiple BAM files with a given reference contained in a single HTML file (rbt plot-bam)

Further functionality is added as it is needed by the authors. Check out the Contributing section if you want contribute anything yourself. For a list of changes, take a look at the CHANGELOG.

Installation

Requirements

Rust-Bio-Tools depends rgsl which needs GSL to be installed:

• Ubuntu: sudo apt-get install libgsl-dev
• Arch: sudo pacman -S gsl
• OSX: brew install gsl

Bioconda

Rust-Bio-Tools is available via Bioconda. With Bioconda set up, installation is as easy as

conda install rust-bio-tools

Cargo

If the Rust compiler and associated Cargo are installed, Rust-Bio-Tools may be installed via

cargo install rust-bio-tools

Source

Download the source code and within the root directory of source run

cargo install

Usage and Documentation

Rust-Bio-Tools installs a command line utility rbt. Issue

rbt --help

for a summary of all options and tools.

Contributing

Any contributions are highly welcome. If you plan to contribute we suggest installing pre-commit hooks. To do so:

1. Install pre-commit as explained here
2. Run pre-commit install in the rust-bio-tools base directory

This should format, check and lint your code when committing.

Authors

• Johannes Köster (https://koesterlab.github.io)
• Felix Mölder
• Henning Timm
• Felix Wiegand