gapfiller
Link to section 'Introduction' of 'gapfiller' Introduction
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length.
BioContainers: https://biocontainers.pro/tools/gapfiller
Home page: https://sourceforge.net/projects/gapfiller/
Link to section 'Versions' of 'gapfiller' Versions
- 2.1.2
Link to section 'Commands' of 'gapfiller' Commands
- GapFiller
Link to section 'Module' of 'gapfiller' Module
You can load the modules by:
module load biocontainers
module load gapfiller
Link to section 'Example job' of 'gapfiller' 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 gapfiller on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gapfiller
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers gapfiller