#bio #tools #bioinformatics

app rust-bio-tools

A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio

36 releases (13 breaking)

0.16.0 Nov 17, 2020
0.14.3 Nov 4, 2020
0.10.3 Jul 1, 2020
0.9.2 Mar 21, 2020
0.2.4 Mar 6, 2018

#76 in Science

Download history 13/week @ 2020-09-16 6/week @ 2020-09-23 55/week @ 2020-09-30 5/week @ 2020-10-07 10/week @ 2020-10-14 42/week @ 2020-10-21 50/week @ 2020-10-28 47/week @ 2020-11-04 86/week @ 2020-11-11 13/week @ 2020-11-18 38/week @ 2020-11-25 4/week @ 2020-12-02 47/week @ 2020-12-09 64/week @ 2020-12-16 1/week @ 2020-12-23 38/week @ 2020-12-30

159 downloads per month

Custom license and GPL-3.0+

3MB
5K SLoC

Rust 4.5K SLoC // 0.0% comments Tera 271 SLoC JavaScript 262 SLoC // 0.2% comments

Rust-Bio-Tools

GitHub Workflow Status

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)

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

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.

Authors

Dependencies

~59MB
~1.5M SLoC