Embarrassingly parallel BLAST search

A quick note: To blast a file with many proteins against a database, you can use recent version of GNU Parallel to fill up all CPUs (which the -num_threads option of BLAST doesn't do, as it only parallelizes some steps of the search):

cat query.fasta | parallel --block 100k --recstart '>' --pipe \ 
    blastp -evalue 0.01 -outfmt 6 -db db.fa -query - > result.tsv

This will split the FASTA file into smaller chunks of about 100 kilobyte, while making sure that the records are valid (i.e. start with an ">").