ORP-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.2.6

Author / Distributor

Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html

Description

From https://oyster-river-protocol.readthedocs.io/en/latest/index.html: "The Oyster River Protocol for (eukaryotic) transcriptome assembly is an actively developed, evidenced based method for optimizing transcriptome assembly. The manuscript corresponding to this protocol is here: https://peerj.com/articles/5428/ In brief, the protocol assembles the transcriptome using a multi-kmer multi-assembler approach, then merges those assemblies into 1 final assembly."

Running Program

Also refer to Running Jobs on Sapelo2

• Version 2.2.6, installed in /apps/singularity-images/

Sample job submission script (sub.sh) to run oyster.mk v. 2.2.6:

#!/bin/bash
#SBATCH --partition=batch
#SBATCH --jobn-name=jobname
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --time=4:00:00
#SBATCH --mem=20gb

singularity run /apps/singularity-images/orp_2.2.6.sif bash -c "source activate orp && /home/orp/Oyster_River_Protocol/oyster.mk \
STRAND=RF \
TPM_FILT=1 \
MEM=15 \
CPU=4 \
READ1=test.1.fq.gz \
READ2=test.2.fq.gz \
RUNOUT=test "

where test.1.fq.gz and test.2.fq.gz are sample data files and need to be replaced by your actual data files. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.

Submit the job to the queue with

sbatch sub.sh

Documentation

Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.htm

Installation

• Version 2.2.6, installed with singularity pull docker://macmaneslab/orp:2.2.6

System

64-bit Linux