Introduction ~~~~~~~~ Dbg2olc is used for efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies.
For more information, please check its website: https://biocontainers.pro/tools/dbg2olc and its home page on Github.
- 20180222
- 20200723
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
You can load the modules by:
module load biocontainers
module load dbg2olcExample job ~~~~~ .. warning:: 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