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With 454 Reads

A few helpful tools to use BLAST with 454 data. Only installed on Fourierseq at the moment.

• bacfish.sh <blast.out> - After running blast on 454 Newbler contigs (usually blastn against nt with an eval of <1e-50, with m=1), you can run this script on the blast output file and it will group your contigs. This was written specifically for sorting out fragment sequencing results of BACs, where you get several contigs and want to quickly validate and bin them into E coli vs. something previously sequenced vs. something new.
• 454blastStats <454reads.fna> - With raw 454 reads in <454reads.fna>, this script will run a high stringency blast against NT and provide a quick-and-dirty frequency plot of top hits. Useful to make sure you sequenced what you thought you were sequencing.

Conversion To GFF (With Track Features)

The script blast2gff.py will convert BLAST results to a GFF file, with track decoration options. You can check the options for the script by running

blast2gff.py --help