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fastascripts
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Manipulate FASTA files
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Download README
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fastascripts
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fastascripts – Manipulate FASTA files ===================================== These scripts were never meant to see the light of day. I apologize for the distasteful code. Utilities ========= * `facanon` Output the lexicographically smaller of the sequence and its reverse complement * `facat` Concatenate FASTA files and add a prefix to the identifier * `fachain` Merge overlapping sequences * `faclean` Reformat and optionally remove short contigs from a FASTA file * `facmp` Compare pairs of sequences * `facstont` Convert colour-space sequence to nucleotides * `fadecimate` Randomly keep 1 in every N pairs of reads * `faget` Select sequences from a FASTA file by identifier * `fagrep` Search a FASTA file using a regular expression * `fakmer` Generate tiled k-mers * `falength` Print the lengths of sequences * `falint` Check the syntax of a FASTA file * `famd5` Calculate a MD5 digest for a FASTA file * `famd5seq` Calculate a MD5 digest for each sequence * `fanttocs` Convert nucleotides to colour-space sequence * `farand` Generate a FASTA file with random sequence * `farc` Reverse and complement the sequences * `farenumber` Renumber the sequences * `faseperate-mates` Separate paired reads into two files * `fasplit-read` Split a read into two at the midpoint * `fastqtofa` Convert a FASTQ file to FASTA format * `fatoagp` Convert FASTA scaffolds to FASTA contigs and an AGP file * `fatofastq` Convert a FASTA file to a FASTQ file * `fatoseq` Remove FASTA headers * `faunamb` Convert IUPAC-IUB ambiguity codes to ACGT * `faunscaffold` Break scaffolds into contigs at Ns License ================================================================================ Copyright 2013 Shaun Jackman ### [ISC License][] 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. [ISC License]: http://opensource.org/licenses/ISC
