Diamond

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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

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/