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 oncoprints from VCF/BCF files (
rbt oncoprint)
Further functionality is added as it is needed by the authors. Any contributions are highly welcome. For a list of changes, take a look at the CHANGELOG.
Rust-Bio-Tools is available via Bioconda. With Bioconda set up, installation is as easy as
conda install rust-bio-tools
If the Rust compiler and associated Cargo are installed, Rust-Bio-Tools may be installed via
cargo install rust-bio-tools
Download the source code and within the root directory of source run
cargo install
Rust-Bio-Tools installs a command line utility rbt. Issue
rbt --help
for a summary of all options and tools.
- Johannes Köster (https://koesterlab.github.io)
- Felix Mölder
- Henning Timm