Oarfish quantifies transcript-level expression from long-read (i.e. Oxford nanopore cDNA and direct RNA and PacBio) sequencing technologies. It handles multi-mapping reads through the use of probabilistic allocation via an expectation-maximization (EM) algorithm.

References:

• Zahra Zare Jousheghani and Rob Patro. Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification. bioRxiv.

• oarfish on GitHub

• Module Name: oarfish (see the modules page for more information)
• Multithreaded using -j/--threads argument.
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • OARFISH_HOME

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load oarfish

[user@cn3144 ~]$ oarfish -j 2 --reads sample1_reads.fq.gz --annotated transcripts.fa --seq-tech ont-cdna -o sample1 --filter-group no-filters --model-coverage
 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. oarfish.sh). For example:

#!/bin/bash
set -e
module load oarfish
oarfish -j ${SLURM_CPUS_PER_TASK:-2} --reads sample1_reads.fq.gz --annotated transcripts.fa --seq-tech ont-cdna -o sample1 --filter-group no-filters --model-coverage

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] oarfish.sh

Create a swarmfile (e.g. oarfish.swarm). For example:

oarfish -j ${SLURM_CPUS_PER_TASK:-2} --reads sample1_reads.fq.gz --annotated transcripts.fa --seq-tech ont-cdna -o sample1 --filter-group no-filters --model-coverage

Submit this job using the swarm command.

swarm -f oarfish.swarm [-g #] [-t #] --module oarfish