Difference between revisions of "ABySS"
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Latest revision as of 21:56, 20 February 2017
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.
Version
- 1.2.7
Authorized Users
CIRCE
account holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
ABySS requires the following module file to run:
apps/abyss/1.2.7
- See Modules for more information.
Running ABySS on CIRCE/SC
The ABySS user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.
- Note on CIRCE: Make sure to run your jobs from your $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
To assemble transcriptome data, see Trans-ABySS.
How to Submit Jobs
Provided are batch scripts for running ABySS as a single processor or multi-processor job. These scripts can be copied into your work directory (the folder with your input files and database files) so that you can submit batch processes to the queue. .
Serial Submit Script
- Single-end assembly
Assemble short reads in a file named reads.fa into contigs in a file named contigs.fa with the following script:
#!/bin/bash # #SBATCH --comment=abyss-test #SBATCH --ntasks=1 #SBATCH --job-name=abyss-test #SBATCH --output=output.%j.abyss-test #SBATCH --time=01:00:00 #### SLURM 1 processor ABySS test to run for 1 hour. module purge module load apps/abyss/1.2.7 ABYSS -k25 reads.fa -o contigs.fa
where ‘-k’ is an appropriate k-mer length. The only method to find the optimal value of ‘k’ is to run multiple trials and inspect the results. The maximum value for ‘k’ is 64.
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ 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
Documentation
Home Page, User Guides, and Manuals
- ABySS Home Page
Benchmarks, Known Tests, Examples, Tutorials, and Other Resources
- ABySS Options
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with ABySS to the IT Help Desk: rc-help@usf.edu