FAST (FAST Analysis of Sequences Toolbox), built on BioPerl, provides 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.
See the FAST Cookbook for examples (https://github.com/tlawrence3/FAST/blob/master/doc/FAST_Cookbook.org) or Lawrence et al. "FAST: FAST Analysis of Sequences Toolbox", to appear (https://github.com/tlawrence3/FAST/blob/master/paper/Lawrence_etal_FAST.pdf).