Racon-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
1.4.13
Author / Distributor
Please see https://github.com/isovic/racon
Description
From https://github.com/isovic/racon: Racon is a "Consensus module for raw de novo DNA assembly of long uncorrected reads. "
Running Program
Also refer to Running Jobs on Sapelo2
For more information on Environment Modules on Sapelo2 please see the Lmod page.
- Version 1.4.13, compiled with GCCcore/8.3.0 toolchain, installed in /apps/eb/Racon/1.4.13-GCCcore-8.3.0
To use this version of racon, please first load the module with
ml Racon/1.4.13-GCCcore-8.3.0
Note: This version does not work on the nodes with AMD Opteron processors. You can request that your job does not get dispatched to a node with AMD Opteron processors by adding the following line to your job submission script:
#SBATCH --constraint=EDR
Sample job submission script (sub.sh) to run racon 1.4.13 in a batch job:
#!/bin/bash #SBATCH --job-name=raconjob #SBATCH --partition=batch #SBATCH --ntasks=1 #SBATCH --cpus-per-task=12 #SBATCH --constraint=EDR #SBATCH --mem=20gb #SBATCH --time=24:00:00 #SBATCH --output=%x.%j.out #SBATCH --error=%x.%j.err cd $SLURM_SUBMIT_DIR ml Racon/1.4.13-GCCcore-8.3.0 racon -t 12 [options]
where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the number of cores per node, the maximum wall clock time, the maximum memory, and the job name need to be modified appropriately as well. Note that if you use the racon option -t to specify using multi threads, please also request the same number of cores with --cpus-per-task. In the example above --cpus-per-task=12 and racon is invoked with -t 12.
Submit the job to the queue with
sbatch sub.sh
Documentation
Please see links from https://github.com/isovic/racon. ml Racon/1.4.13-GCCcore-8.3.0 racon -h usage: racon [options ...] <sequences> <overlaps> <target sequences> #default output is stdout <sequences> input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences used for correction <overlaps> input file in MHAP/PAF/SAM format (can be compressed with gzip) containing overlaps between sequences and target sequences <target sequences> input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences which will be corrected options: -u, --include-unpolished output unpolished target sequences -f, --fragment-correction perform fragment correction instead of contig polishing (overlaps file should contain dual/self overlaps!) -w, --window-length <int> default: 500 size of window on which POA is performed -q, --quality-threshold <float> default: 10.0 threshold for average base quality of windows used in POA -e, --error-threshold <float> default: 0.3 maximum allowed error rate used for filtering overlaps --no-trimming disables consensus trimming at window ends -m, --match <int> default: 3 score for matching bases -x, --mismatch <int> default: -5 score for mismatching bases -g, --gap <int> default: -4 gap penalty (must be negative) -t, --threads <int> default: 1 number of threads --version prints the version number -h, --help prints the usage
Installation
Downloaded from https://github.com/lbcb-sci/racon/
System
64-bit Linux