dbg2olc
Link to section 'Introduction' of 'dbg2olc' 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.
Link to section 'Versions' of 'dbg2olc' Versions
- 20180222
- 20200723
Link to section 'Commands' of 'dbg2olc' 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
Link to section 'Module' of 'dbg2olc' Module
You can load the modules by:
module load biocontainers
module load dbg2olc
Link to section 'Example job' of '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