README.md

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