USEARCH

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 ./
usearch8.0.1623 -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!"

Additional USEARCH documentation may be found on USEARCH web site.