Purdue University

Commands

• AssemblyStatistics
• DBG2OLC
• RunSparcConsensus.txt
• SelectLongestReads
• SeqIO.py
• Sparc
• SparseAssembler
• split_and_run_sparc.sh
• split_and_run_sparc.sh.bak
• split_reads_by_backbone.py

Module

You can load the modules by:

module load biocontainers
module load dbg2olc

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Dbg2olc on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=dbg2olc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers dbg2olc

SelectLongestReads sum 600000000 longest 0 o TEST.fq f SRR1976948.abundtrim.subset.pe.fq