bioinfo-scripts

Collection of bioinformatics utility scripts, mostly written in Bioperl

Naming convention

• fa-* - scripts for FASTA files
• fq-* - scripts for FASTQ files (4 line format only)
• gb-* or genbank* - scripts for GENBANK files (sometimes EMBL via --format option)
• fx-* - scripts that work on FASTA or FASTQ
• blast* - scripts that work on standard BLAST output
• gff* - scripts for GFF format (usually version 3.0 but check --gffver option)
• faa-* - scripts for proteins / amino-acid FASTA files

Other scripts

• gene-puller.pl - extract and align amplicons from sets of contigs
• genbank2krakenlib.pl - Convert Genbank file(s) into Kraken FASTA files

Advice

Some of these scripts were written as early as 2004. Use them to get out of a bind, for educational reasons, or as a basis for something more robust.