Difference between revisions of "Diamond"
(Created page with "This is very fast alternative to the blastx program. This page contains some details about the program == key points made== * Describes blastx as the "gold standard" * high...") |
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* Describes blastx as the "gold standard" | * Describes blastx as the "gold standard" | ||
* highest value placed on sensitivity | * 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 $NSLOTS -b 5 -d N95 -q 4440037.3.dna.fa -a N95 -t temp -e 0.000001 -k 1 -f tab | ||
| + | diamond view -a N95.daa -o N95.m8 | ||
Revision as of 10:34, 21 April 2016
This is very fast alternative to the blastx program. This page contains some details about the program
key points made
- Describes blastx as the "gold standard"
- highest value placed on sensitivity
Running in gridengine
Here's a workable script
#!/bin/bash #$ -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
