====Quast====

QUAST stands for **QU**ality **AS**sessment **T**ool. The tool evaluates genome assemblies by computing various metrics. Quast was developed by the Algorithmic Biology Lab at the St. Petersburg Academic University of the Russian Academy of Sciences. For more documentation on Quast click [[http://bioinf.spbau.ru/quast|here]]

====Enviornment Setup====

Quast is used as a python command line tool, so we will need to load the ''python'' module to run the script, do this by adding this line to either the ''.bashrc'' file or the ''PBS'' script when you run your tests.

<code>
module load python
</code>

Create a directory to run the Quast jobs and copy the test data from the Quast version folder as shown below.

<code>
razor-l2:jokinsey:~$ mkdir QUAST-JOBS
razor-l2:jokinsey:~$ cd QUAST-JOBS/
razor-l2:jokinsey:~/QUAST-JOBS$ cp -r /share/apps/quast/quast-3.1/test_data/ .
</code>

====Serial Example====

Inside your ''$HOME/QUAST-JOBS'' directory create a ''PBS'' script named ''quastTest.pbs'' with the information below, to run Quast on the sample inputs.

<code>
#!/bin/bash
#PBS -N Quast
#PBS -q tiny12core
#PBS -j oe
#PBS -m abe
#PBS -M jokinsey@uark.edu
#PBS -o Quast.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:10:00

cd $PBS_O_WORKDIR
cp -r test_data/ /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

python /share/apps/quast/quast-3.1/quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff
mv /scratch/$PBS_JOBID/quast_results/results* $PBS_O_WORKDIR/quast_results/
</code>

This script will run Quast on the inputs located in the ''/scratch/$PBS_JOBID'' directory. If you would like to know more about the values and flags used refer to the manual [[http://quast.bioinf.spbau.ru/manual.html|here]].

The output for the job should be located in ''$HOME/QUAST-JOBS/quast_results/results_<when_the_job_was_submitted>''. 

All thats left is to submit the job.

<code>
razor-l2:jokinsey:~/QUAST-JOBS$ qsub quastTest.pbs
</code>

We did not specify an output directory therefore Quast will create a directory ''quast_results/results_<DATE>'' where the output of the job will be stored. It will also create a directory ''quast_results/latest'' where the most recent job's output will be stored.

Many files will be given as output, and all of there descriptions are listed in the [[http://quast.bioinf.spbau.ru/manual.html|manual]]. A simplified listing of the output will be in the ''report.txt'' file.

====Parallel Example====

When Quast is run it will determine the number of available processors which we specify in the ''PBS'' script with the value of ''ppn''. Quast also allows manual specification of the number of allowed threads, which can decrease the time of the job. Change the ''PBS'' script above to include thread specification.

<code>
#!/bin/bash
#PBS -N Quast
#PBS -q tiny12core
#PBS -j oe
#PBS -m abe
#PBS -M jokinsey@uark.edu
#PBS -o Quast.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:10:00

cd $PBS_O_WORKDIR
cp -r test_data/ /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

python /share/apps/quast/quast-3.1/quast.py --threads 12 test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff
mv /scratch/$PBS_JOBID/quast_results/results* $PBS_O_WORKDIR/quast_results/
</code>

This changes the maximum thread count to 12 as we don't want to run more threads on a node than their are cores on that node, because with hyper-threading turned off any more would kill efficiency.