Diamond

This is very fast alternative to the blastx and blastp program. This page contains some details about the program

key points made

• Describes blastx as the "gold standard"
• highest value placed on sensitivity

Diamond databases for nr and swissprot are already made and are in:

/shelf/public/blastntnr/blastDatabases/

nr.dmnd   uniprot.dmnd

These two will work with "module load diamond"

However, the latest diamond will only work with: nr_PT.dmnd

Diamond website look here for detailed use:

https://github.com/bbuchfink/diamond

Running in gridengine

Here's a workable script

#!/bin/bash 
#$ -cwd 
#$ -j y
#$ -S /bin/bash 
#$ -V
#$ -q single.q
#$ -pe multi 16
module load diamond
diamond blastx -p $NSLOTS -b 5 -d N95 -q 4440037.3.dna.fa -a N95 -t temp -e 0.000001 -k 1 -f tab 
diamond view -a N95.daa -o N95.m8

A Diamond nr database and Swissprot database is already made in here:

/shelf/public/blastntnr/blastDatabases/

uniprot.dmnd and nr.dmnd

taxonomically annotate a diamond tab output

Use this: https://github.com/peterthorpe5/public_scripts/tree/master/Diamond_BLAST_add_taxonomic_info

All files requires for this are already made in

/shelf/public/blastntnr/blastDatabases/