Practical Haplotype Graph (PHG) is a general, graph-based, computational framework that can be used with a variety of skim sequencing methods to infer high-density genotypes directly from low-coverage sequence.
For more information, please check:
Docker hub: https://hub.docker.com/r/maizegenetics/phg
Home page: https://www.maizegenetics.net/phg
- 1.0
- CreateConsensi.sh
- CreateHaplotypes.sh
- CreateReferenceIntervals.sh
- CreateSmallDataSet.sh
- CreateValidIntervalsFile.sh
- IndexPangenome.sh
- LoadAssemblyAnchors.sh
- LoadGenomeIntervals.sh
- ParallelAssemblyAnchorsLoad.sh
- RunLiquibaseUpdates.sh
- CreateHaplotypesFromBAM.groovy
- CreateHaplotypesFromFastq.groovy
- CreateHaplotypesFromGVCF.groovy
You can load the modules by:
module load biocontainers module load phg
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 phg on our clusters:
#!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=phg #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge ml biocontainers phg