ABySS

Description

From the ABySS web site: ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

• ABySS Home Page

Version

• 1.2.7

Authorized Users

• CIRCE account holders

Platforms

• CIRCE cluster

Running ABySS Jobs on CIRCE

To assemble transcriptome data, see Trans-ABySS.

Modules

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

• apps/abyss/1.2.7

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

How to Submit Jobs

Provided are batch scripts for running ABySS as a single processor or multi-processor job. These scripts 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. For help on submitting jobs to the queue, see our SLURM User’s Guide. These scripts are provided as examples only. Your SLURM and ABySS options will vary.

Please refer to the Additional Documentation section for a link to ABySS option information.

Serial Submit Script

• Single-end assembly

Assemble short reads in a file named reads.fa into contigs in a file named contigs.fa with the following script:

#!/bin/bash
#
#SBATCH --comment=abyss-test
#SBATCH --ntasks=1
#SBATCH --job-name=abyss-test
#SBATCH --output=output.%j.abyss-test
#SBATCH --time=01:00:00

#### Slurm 1 processor ABySS test to run for 1 hour.

module purge
module load apps/abyss/1.2.7

ABYSS -k25 reads.fa -o contigs.fa

 
where ‘-k’ is an appropriate k-mer length. The only method to find the optimal value of ‘k’ is to run multiple trials and inspect the results. The maximum value for ‘k’ is 64.  
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 ./abyss-test.sh

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

Distributed Parallel

• Paired-end assembly

To assemble paired short reads in two files named reads1.fa and reads2.fa into contigs in a file named ecoli-contigs.fa, use the script:

#!/bin/bash
#
#SBATCH --comment=abyss-test
#SBATCH --ntasks=8
#SBATCH --job-name=abyss-test
#SBATCH --output=output.%j.abyss-test
#SBATCH --time=01:00:00

#### Slurm 8 processor ABySS test to run for 1 hour.

module purge
module load apps/abyss/1.2.7

abyss-pe k=25 n=10 in='reads1.fa reads2.fa' name=ecoli

 
where ‘k’ is the k-mer length as before. ‘n’ is the minimum number of pairs needed to consider joining two contigs. The optimal value for ‘n’ must be found by trial. ‘in’ specifies the input files to read, which may be in FASTA, FASTQ, qseq, export, SAM or BAM format and compressed with gz, bz2 or xz and may be tarred. The assembled contigs will be stored in ${name}-contigs.fa.

The suffix of the read identifier for a pair of reads must be one of ‘1’ and ‘2’, or ‘A’ and ‘B’, or ‘F’ and ‘R’, or ‘F3’ and ‘R3’, or ‘forward’ and ‘reverse’. The reads may be interleaved in the same fileor found in different files. If the mates are in different files, it’s highly recommended to place each pair of files adjacent on the command line and to use an even number of threads. Even if you are running on a single-processor machine, using two threads will help performance. Do not group together all the files containing the forwards reads followed by all the files containing the reverse reads.

Reads without mates should be placed in a file specified by the ‘se’
(single-end) parameter. Reads without mates in the paired-end files
will slow down the paired-end assembler considerably during the
ParseAligns stage.

See also Trans-ABySS.

 
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 ./abyss-test.sh

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

Additional Documentation

• ABySS Options
  • http://seqanswers.com/wiki/ABySS#Single-end_assembly

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

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