ContigExtender (contig-extender)
Overview
ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.
As stated in their github page, ContigExtender requires Docker. CSF3 has Singularity installed for supporting containerised application therefore ContigExtender Singularity image was built for users using the master branch of git repository available as on 7th February, 2025.
Restrictions on use
ContigExtender is open source and freely distributed. It is released under GPL-3.0 license.
Please follow this link for further information – GPL-3.0 license
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this.
To use the software you must the modulefile:
module load apps/singularity/contig_extender/default
Examples
Examples that came along with this git repository are available in CSF3 under the following directory:
$APPDIR/examples
Users can copy the examples folder to their work directory and run them using the sample jobscript below for testing by first loading the module and then running the command:
cp -r $APPDIR/examples .
Running the application
Please do not run ContigExtender on the login node. Jobs should be submitted to the compute nodes via batch using jobscript.
Ideally, ContigExtender should be run in a parallel environment. By default, it will use 8 CPU cores/threads, if not set separately using the flag: --threads [THREADS]
Users must specify the number of CPU cores they want to use for the job in their jobscript in the line/flag #$ -pe amd.pe 4 and then add --threads $NSLOTS in the singularity command line as shown in the jobscript below:
Parallel batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory #$ -pe amd.pe 4 # Set the number of CPU required for the job # Load the version you require module load apps/singularity/contig_extender/default singularity exec --bind /scratch:/scratch,/opt:/opt $CONTIG_EXTENDER_SIF python3 /app/extender/extender_wrapper.py --threads $NSLOTS examples/BKV_seed_1000_867.fa examples/BKV_250_50_0.01_0_.fastq
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.