NAME

FAST - FAST Analysis of Sequences Toolbox

VERSION

Version 1.03

SYNOPSIS

The Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records. Modeled after the UNIX textutils (such as grep, cut, head, tr, etc), FAST workflows are designed for "inline" (serial) processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm.

UTILITIES

FAST 1.0x contains the following utilities. Each has its own man page.

alncut select sites based on site variation and gap-content

alnpi calculate molecular population genetic statistics

fascodon tally/annotate codon usage

fascomp tally/annotate monomer frequencies

fasconvert convert sequences to or from from fasta format

fascut select/reorder sequence records based on index lists/ranges

fasfilter filter sequence records based on numerical values

fasgrep filter sequence records based on perl regular expressions

fashead filter leading sequence records

faslen annotate sequence lengths

faspaste concatenate sequence records

fasrc reverse complement nucleotide sequences and alignments

fassort sort sequence records

fassub transform sequence records using regex-based substitutions

fastail filter trailing sequence records

fastax filter sequence records based on NCBI taxonomy IDs or names

fastaxsort sort sequence records based on NCBI taxonomy IDs or names

fastr transform sequence records by character, degap, strict

fasuniq remove duplicate sequence records from sorted data

faswc tally sequences and characters

fasxl translate gapped and ungapped sequences and alignments

gbfalncut select sites by regex matching of features in a GenBank file

gbfcut print sequences by regex matching to features in a GenBank file

AUTHORS

David H. Ardell, <dhard at cpan.org> and members of the Ardell Laboratory and other contributors including: Travis Lawrence Dana Carper Katherine Amrine Kyle Kauffman Claudia Canales

BUGS

Please report any bugs or feature requests to bug-fast at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=FAST. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2015 David H. Ardell.

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

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