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ART on Biowulf

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. VarSim) for evaluating variant calling tools or methods.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load art
[user@cn3144 ~]$ cp -r /usr/local/apps/art/examples /data/$USER
[user@cn3144 ~]$ cd /data/$USER/examples
[user@cn3144 ~]$ art_454 -a -s ./testSeq.fa ./single_454_flx 10
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. art.sh) : For example:

module load art
cd /data/$USER/examples
art_454 -a -s ./testSeq.fa ./single_454_flx 10

Submit this job using the Slurm sbatch command.

sbatch --mem=5g art.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit set of independent commands requiring identical resources.

Create a swarmfile (e.g. art.swarm).

cd /data/$USER/examples1; art_454 -a -s ./testSeq.fa ./single_454_flx 10
cd /data/$USER/examples2; art_454 -a -s ./testSeq.fa ./single_454_flx 10
cd /data/$USER/examples3; art_454 -a -s ./testSeq.fa ./single_454_flx 10
cd /data/$USER/examples4; art_454 -a -s ./testSeq.fa ./single_454_flx 10

Submit this job using the swarm command.

swarm -f art.swarm -g 5 --module art
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module art Loads the TEMPLATE module for each subjob in the swarm