Oases

Description

From the Oases home page: Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. Oases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called “loci”. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.

Oases Home Page

Version

0.1.22

Authorized Users

CIRCE account holders

Platforms

CIRCE cluster

Running Oases Jobs on CIRCE

Modules

Before running a job, you must first set up your environment properly. Here are the required module files:

apps/oases/0.1.22

To run Oases on the cluster, ensure that you use module add prior to using any executables. See Modules for more information.

How to Submit Jobs

Provided is a batch script for running Oases executables on the cluster. This script can be copied into your work directory (the folder with your input files and database files) so that you can submit batch processes to the queue.

Serial Submit Script

You must first process the reads using Velvet:

you must choose a hash length at this stage (cf. the Velvet manual),
DO NOT set a coverage cutoff, you should set that when running oases,
DO NOT set an expected coverage,
remember to turn on the -read_trkg option when running velvetg.

You can run Oases on your data working directory after it has been created and processed by Velvet. Provide all the information about insert lengths and their standard deviation as possible (identical to Velvet)

An example of processing in velvet (using “test_reads.fa” from the known tests directory listed below) is:

[johndoe@login1 ~]$ mkdir /work/j/johndoe/oases
[johndoe@login1 ~]$ mkdir /work/j/johndoe/oases/data
[johndoe@login1 ~]$ cd /work/j/johndoe/oases
[johndoe@login1 mega]$ cp /opt/apps/oases/0.1.22/data/test_reads.a /work/j/johndoe/oases/data
[johndoe@login1 mega]$ velveth /work/j/johndoe/oases/data 21 -shortPaired /work/j/johndoe/oases/data/test_reads.fa
[johndoe@login1 mega]$ velvetg /work/j/johndoe/oases/data/ -read_trkg yes
[johndoe@login1 mega]$

You will then be ready to process the data directory with Oases.

If, for example, you wrote your velveth/velvetg output to $WORK/oases/data, you would set up a submit script like this:

The script below (for testing, name it “oases-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.

#!/bin/bash
#
#SBATCH --comment=oases-test
#SBATCH --ntasks=4
#SBATCH --job-name=oases-test
#SBATCH --output=output.%j.oases-test
#SBATCH --time=01:00:00

#### Slurm 4 processor Oases test to run for 1 hour.

module add apps/oases/0.1.22
oases $WORK/data -ins_length 200

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./oases-test.sh

You can view the status of your job with the “squeue -u <username>” command

Additional Documentation

Oases Manual
- /opt/apps/oases/0.1.22/MANUAL.txt
Oases Runtime Options
- http://www.ebi.ac.uk/~zerbino/oases/Manual.txt
Oases Known Tests
- /opt/apps/oases/0.1.22/data

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Oases to the IT Help Desk: rc-help@usf.edu