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:
- Install
pre-commitas explained here - Run
pre-commit installin the rust-bio-tools base directory
This should format, check and lint your code when committing.