BLAST
Tips to accelerate your blast (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) search on computer cluster like Cedar:
- try copying your blast database fasta to local node ramdisk (/tmp on cedar i think) and run makeblastdb at beginning of script on node to generate your blast db on ramdisk
- use multi-threading even if not so effficient implementation in blast (option -num_threads)
- Lower number of hits returned if applicable (-max_target_seqs and also -max_hsps option can help)
- Try also limiting your hit list using evalue filters (if applicable) to near identical hits (-evalue )