FAST: FAST Analysis of Sequences Toolbox

FAST (FAST Analysis of Sequences Toolbox), built on BioPerl, provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU’s Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can facilitate better documentation and reproducibility of bioinformatic protocols, supporting better transparency in big biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R and GenBank, help make FAST easy to learn. FAST automates numerical, text-based, sequence-based and taxonomic searching, sorting, selection and transformation of sequence records and alignment sites based on indices, ranges, tags and feature annotations, and analytics for composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics makes FAST useful for molecular evolutionary analysis. FAST is portable, easy to install, and secure, with stable releases posted to CPAN and development on Github. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FASTQ formatted files are also supported. The command-line basis of FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

Dependencies and Installation

FAST does not require its users to know Perl or BioPerl, just the Unix shell. However, FAST has Perl Module dependencies. The easiest way to install FAST is with CPAN, Perl’s package manager, with the following command: perl -MCPAN -e 'install FAST' which may require superuser privileges on your system.

Getting Started

Even after installing FAST using CPAN, it is worth manually downloading and opening the FAST installer package from its CPAN page because it provides example data to use with examples given in the FAST utility man pages and the FAST Cookbook.

Licensing and Attribution

The FAST project is distributed under the terms of the Artistic License 2.0.

Please cite Lawrence et al. (2015) and Stajich et al. (2002).The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12(10):1611-8 in all scientific works that use FAST.

Release Notes

The most recent version is 1.02 released February, 2015.