shorah
Link to section 'Introduction' of 'shorah' Introduction
Shorah is an open source project for the analysis of next generation sequencing data.
For more information, please check its website: https://biocontainers.pro/tools/shorah and its home page on Github.
Link to section 'Versions' of 'shorah' Versions
- 1.99.2
Link to section 'Commands' of 'shorah' Commands
- shorah
- b2w
- diri_sampler
- fil
Link to section 'Module' of 'shorah' Module
You can load the modules by:
module load biocontainers
module load shorah
Link to section 'Example job' of 'shorah' 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 Shorah on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=shorah
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers shorah
shorah amplicon -b ampli_sorted.bam -f reference.fasta
shorah shotgun -b test_aln.cram -f test_ref.fasta
shorah shotgun -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:42-272 -R 42 -b test_aln.cram -f ref.fasta