James: Created page with "USEARCH (64 bit version) is installed on Penzias HPC cluster. To start using USEARCH load corresponding module first:

 module load usearch

Example SLURM script that can be used to submit a job with a typical USEARCH workflow is shown below:

 #!/bin/bash #SBATCH --partition production #SBATCH --job-name usearch_x #SBATCH --nodes=1 #SBATCH --ntasks=1   cd $SLURM_SUBMIT_DIR echo "Starting..." cp /share/apps/usearch/8.0.1623/sample/reads.fq ./ usearch8..."

2022-10-20T20:23:30Z

Created page with "USEARCH (64 bit version) is installed on Penzias HPC cluster. To start using USEARCH load corresponding module first: <pre> module load usearch </pre> Example SLURM script that can be used to submit a job with a typical USEARCH workflow is shown below: <pre> #!/bin/bash #SBATCH --partition production #SBATCH --job-name usearch_x #SBATCH --nodes=1 #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR echo "Starting..." cp /share/apps/usearch/8.0.1623/sample/reads.fq ./ usearch8..."

New page

USEARCH (64 bit version) is installed on Penzias HPC cluster. To start using USEARCH
load corresponding module first:
<pre>
module load usearch
</pre>

Example SLURM script that can be used to submit a job with a typical USEARCH workflow
is shown below:
<pre>
#!/bin/bash
#SBATCH --partition production
#SBATCH --job-name usearch_x
#SBATCH --nodes=1
#SBATCH --ntasks=1

cd $SLURM_SUBMIT_DIR
echo "Starting..."
cp /share/apps/usearch/8.0.1623/sample/reads.fq ./
usearch8.0.1623 -fastq_filter reads.fq -fastaout reads.fa
usearch8.0.1623 -derep_fulllength reads.fa -fastaout derep.fa -sizeout
usearch8.0.1623 -sortbysize derep.fa -fastaout sorted.fa -minsize 1
usearch8.0.1623 -cluster_otus sorted.fa -otus otus1.fa -relabel OTU_ -sizeout -uparseout results.txt
echo "Done!"
</pre>

Additional USEARCH documentation may be found on [http://www.drive5.com/usearch/manual USEARCH web site].

USEARCH - Revision history