ORP-Sapelo2: Difference between revisions
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Sapelo2 | Sapelo2 | ||
=== Version === | === Version === | ||
2.2.6 | 2.2.6, 2.2.8 | ||
===Author / Distributor=== | ===Author / Distributor=== | ||
Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html | Please see https://oyster-river-protocol.readthedocs.io/en/latest/index.html |
Latest revision as of 16:45, 13 May 2024
Category
Bioinformatics
Program On
Sapelo2
Version
2.2.6, 2.2.8
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 --job-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