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(Created page with "==Application Details== * Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence d...")
 
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* Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.  
 
* Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.  
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* Version: 2.4.0
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* Version: 2.4.0 , 2.6.0
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* Modules: ncbi-blast/2.4.0
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* Modules: ncbi-blast/2.4.0, ncbi-blast/2.6.0
 
* Licence: Open-source (BLAST is a registered trademark of the National Library of Medicine)
 
* Licence: Open-source (BLAST is a registered trademark of the National Library of Medicine)
  
 
==Usage Examples==
 
==Usage Examples==
 +
  
 
===Command Set===
 
===Command Set===
  
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{| class="wikitable"
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ncbi-blast provides the following commands:
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| style="width:50%" | <Strong></Strong>
 
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| style="width:50%" | <Strong></Strong>
 
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|-
 
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| [[Applications|Applications]]
 
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| How to use the application modules that are available on Viper.
 
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|-
 
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| [[General|General]]
 
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| General information about using Viper.
 
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|-
 
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| [[Training|Training]]
 
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| Training information about how to extend your knowledge of using Viper.
 
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|-
 
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| [[Programming|Programming]]
 
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| Programming support on writing and compiling programs in a range of different languages available.
 
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|-
 
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|}
 
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blastdb_aliastool 
 
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blastdbcmd     
 
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blastn 
 
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blastx           
 
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deltablast 
 
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legacy_blast.pl 
 
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makembindex   
 
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psiblast 
 
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rpstblastn 
 
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tblastn 
 
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update_blastdb.pl
 
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blastdbcheck     
 
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blast_formatter 
 
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blastp 
 
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convert2blastmask 
 
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dustmasker 
 
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makeblastdb     
 
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makeprofiledb 
 
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rpsblast 
 
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segmasker 
 
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tblastx 
 
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windowmasker
 
  
 +
* blast_formatter 
 +
* blastdb_aliastool 
 +
* blastdbcheck     
 +
* blastdbcmd     
 +
* blastn 
 +
* blastp 
 +
* blastx           
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* convert2blastmask 
 +
* deltablast 
 +
* dustmasker 
 +
* legacy_blast.pl 
 +
* makeblastdb     
 +
* makembindex   
 +
* makeprofiledb 
 +
* psiblast 
 +
* rpsblast 
 +
* rpstblastn 
 +
* segmasker 
 +
* tblastn 
 +
* tblastx 
 +
* update_blastdb.pl
 +
* windowmasker
  
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
 
  
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[username@login] module load abyss/1.5.2/gcc-4.9.3
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===Interactive Session===
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[username@login] wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
 
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[username@login] tar xzvf test-data.tar.gz
 
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[username@login} abyss-pe k=25 name=test \
 
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    in='test-data/reads1.fastq test-data/reads2.fastq'
 
  
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</pre>
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<pre style="background-color: #000; color: white; font-family: monospace, sans-serif;">
  
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===Calculate assembly contiguity statistics===
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[username@login01 ~]$ interactive
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salloc: Granted job allocation 3619736
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
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Job ID 3619736 connecting to c081, please wait...
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c081.vc-main
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[username@login] module load abyss/1.5.2/gcc-4.9.3
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[username@c081 ~]$ module add ncbi-blast/2.
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[username@login] abyss-fac test-unitigs.fa
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ncbi-blast/2.11.0  ncbi-blast/2.12.0  ncbi-blast/2.4.0  ncbi-blast/2.6.0
 +
[username@c081 ~]$ module add ncbi-blast/2.6.0
 +
[username@c081 ~] blastp <user options>
  
 
</pre>
 
</pre>
  
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===Parallel processing===
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===Batch Script===
  
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The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single machine. To use multiple machines for assembly, you must create a hostfile for mpirun, which is described in the mpirun man page.
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
  
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Do not run '''mpirun -np 8 abyss-pe'''. To run ABySS with 8 threads, use '''abyss-pe np=8'''. The abyss-pe driver script will start the MPI process, like so: '''mpirun -np 8 ABYSS-P.'''
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#!/bin/bash
  
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The paired-end assembly stage is multithreaded, but must run on a single machine. The number of threads to use may be specified with the parameter j. The default value for j is the value of np.
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#SBATCH -J blast
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#SBATCH -N 1
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#SBATCH --ntasks-per-node 1
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#SBATCH -o job-%j.out
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#SBATCH -e job-%j.out
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#SBATCH -p compute
  
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'''Note''': this example is done on a high memory node, usually access would be achieved with the scheduler
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# perfoms NR blast (blastx)
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infile="$1"
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
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outfile="$(basename "${infile%.*}").xml"
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database="/swissprot/uniprot_sprot"
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[username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3
 
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[username@c230 ~]$ mpirun abyss-pe np=40
 
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</pre>
 
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Through '''SLURM''' this would become the script:
 
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
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#!/bin/bash
 
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#SBATCH -J abyss
 
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#SBATCH -p highmem
 
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#SBATCH -N 2
 
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#SBATCH --ntasks-per-node=40
 
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#SBATCH -o %N.%j.%a.out
 
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#SBATCH -e %N.%j.%a.err
 
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#SBATCH --exclusive
 
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#SBATCH -t 00:30:00
 
  
 
module purge
 
module purge
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module load abyss/1.5.2/gcc-4.9.3
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module load ncbi-blast/2.6.0
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#Run your ABySS commands
 
  
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abyss-pe name=test k=48 n=8 in='test-1.fa test-3.fa'
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blastp \
 +
-query "${infile}" \
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-db "${database}" \
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-out "${outfile}".xml \
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-evalue 1e-5 \
 +
-num_threads 8 \
 +
-max_target_seqs 50 \
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-outfmt 5
  
 
</pre>
 
</pre>
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==Further Information==
 
==Further Information==
  
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* [http://computing.bio.cam.ac.uk/local/doc/abyss.html http://computing.bio.cam.ac.uk/local/doc/abyss.html]
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* [https://blast.ncbi.nlm.nih.gov/Blast.cgi https://blast.ncbi.nlm.nih.gov/Blast.cgi]
  
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{|
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{{Modulepagenav}}
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|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
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|style="width:95%; border-width: 0" |
 
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* [[Main_Page|Home]]
 
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* [[Applications|Application support]]
 
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* [[General|General]]
 
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* [[Training|Training]]
 
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* [[Programming|Programming support]]
 
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|-
 
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|}
 

Latest revision as of 12:11, 17 November 2022

Application Details

  • Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
  • Version: 2.4.0 , 2.6.0
  • Modules: ncbi-blast/2.4.0, ncbi-blast/2.6.0
  • Licence: Open-source (BLAST is a registered trademark of the National Library of Medicine)

Usage Examples

Command Set

ncbi-blast provides the following commands:

  • blast_formatter
  • blastdb_aliastool
  • blastdbcheck
  • blastdbcmd
  • blastn
  • blastp
  • blastx
  • convert2blastmask
  • deltablast
  • dustmasker
  • legacy_blast.pl
  • makeblastdb
  • makembindex
  • makeprofiledb
  • psiblast
  • rpsblast
  • rpstblastn
  • segmasker
  • tblastn
  • tblastx
  • update_blastdb.pl
  • windowmasker


Interactive Session


[username@login01 ~]$ interactive
salloc: Granted job allocation 3619736
Job ID 3619736 connecting to c081, please wait...
c081.vc-main
[username@c081 ~]$ module add ncbi-blast/2.
ncbi-blast/2.11.0  ncbi-blast/2.12.0  ncbi-blast/2.4.0   ncbi-blast/2.6.0
[username@c081 ~]$ module add ncbi-blast/2.6.0
[username@c081 ~] blastp <user options>

Batch Script


#!/bin/bash

#SBATCH -J blast
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -o job-%j.out
#SBATCH -e job-%j.out
#SBATCH -p compute

# perfoms NR blast (blastx)
infile="$1"
outfile="$(basename "${infile%.*}").xml"
database="/swissprot/uniprot_sprot"

module purge
module load ncbi-blast/2.6.0

blastp \
 -query "${infile}" \
 -db "${database}" \
 -out "${outfile}".xml \
 -evalue 1e-5 \
 -num_threads 8 \
 -max_target_seqs 50 \
 -outfmt 5

Further Information





Modules | Main Page | Further Topics

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