86 releases
0.42.2 | Apr 10, 2024 |
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0.42.0 | Jan 18, 2023 |
0.41.0 | Aug 23, 2022 |
0.40.0 | Jul 21, 2022 |
0.2.4 | Mar 6, 2018 |
#18 in Biology
4,199 downloads per month
3MB
8K
SLoC
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-commit
as explained here - Run
pre-commit install
in the rust-bio-tools base directory
This should format, check and lint your code when committing.
Authors
Dependencies
~90MB
~1.5M SLoC