Difference between revisions of "Diamond"
PeterThorpe (talk | contribs) (→key points made) |
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| − | This is very fast alternative to the blastx program. This page contains some details about the program | + | This is very fast alternative to the blastx and blastp program. This page contains some details about the program |
== key points made== | == key points made== | ||
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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 | ||
| + | |||
| + | 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= | = Running in gridengine= | ||
| Line 20: | Line 33: | ||
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 blastx -p $NSLOTS -b 5 -d N95 -q 4440037.3.dna.fa -a N95 -t temp -e 0.000001 -k 1 -f tab | ||
diamond view -a N95.daa -o N95.m8 | diamond view -a N95.daa -o N95.m8 | ||
| + | |||
| + | |||
| + | A Diamond nr database and Swissprot database is already made in here: | ||
| + | |||
| + | /shelf/public/blastntnr/blastDatabases/ | ||
| + | |||
| + | uniprot.dmnd and nr.dmnd | ||
| + | |||
| + | = taxonomically annotate a diamond tab output = | ||
| + | |||
| + | Use this: | ||
| + | https://github.com/peterthorpe5/public_scripts/tree/master/Diamond_BLAST_add_taxonomic_info | ||
| + | |||
| + | All files requires for this are already made in | ||
| + | |||
| + | /shelf/public/blastntnr/blastDatabases/ | ||
Latest revision as of 13:39, 22 January 2019
This is very fast alternative to the blastx and blastp program. This page contains some details about the program
key points made
- Describes blastx as the "gold standard"
- highest value placed on sensitivity
Diamond databases for nr and swissprot are already made and are in:
/shelf/public/blastntnr/blastDatabases/ nr.dmnd uniprot.dmnd
These two will work with "module load diamond"
However, the latest diamond will only work with: nr_PT.dmnd
Diamond website look here for detailed use:
https://github.com/bbuchfink/diamond
Running in gridengine
Here's a workable script
#!/bin/bash #$ -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/
