rust-bio-tools 0.8.1

A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio.
rust-bio-tools-0.8.1 is not a library.

Rust-Bio-Tools

Travis

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 call-consensus-reads bam|fastq)

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.

Installation

Bioconda

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

conda install rust-bio-tools

Manual

Download the source code and issue

cargo install

from the root directory of the source.

Usage and Documentation

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

rbt --help

for a summary of all options and tools.

Authors