These scripts were never meant to see the light of day. I apologize for the distasteful code.
facanonOutput the lexicographically smaller of the sequence and its reverse complementfacatConcatenate FASTA files and add a prefix to the identifierfachainMerge overlapping sequencesfacleanReformat and optionally remove short contigs from a FASTA filefacmpCompare pairs of sequencesfacstontConvert colour-space sequence to nucleotidesfadecimateRandomly keep 1 in every N pairs of readsfagetSelect sequences from a FASTA file by identifierfagrepSearch a FASTA file using a regular expressionfakmerGenerate tiled k-mersfalengthPrint the lengths of sequencesfalintCheck the syntax of a FASTA filefamd5Calculate a MD5 digest for a FASTA filefamd5seqCalculate a MD5 digest for each sequencefanttocsConvert nucleotides to colour-space sequencefarandGenerate a FASTA file with random sequencefarcReverse and complement the sequencesfarenumberRenumber the sequencesfaseperate-matesSeparate paired reads into two filesfasplit-readSplit a read into two at the midpointfastqtofaConvert a FASTQ file to FASTA formatfatoagpConvert FASTA scaffolds to FASTA contigs and an AGP filefatofastqConvert a FASTA file to a FASTQ filefatoseqRemove FASTA headersfaunambConvert IUPAC-IUB ambiguity codes to ACGTfaunscaffoldBreak scaffolds into contigs at Ns
Copyright 2013 Shaun Jackman
Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.