phg
Link to section 'Introduction' of 'phg' Introduction
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.
Docker hub: https://hub.docker.com/r/maizegenetics/phg
Home page: https://www.maizegenetics.net/phg
Link to section 'Versions' of 'phg' Versions
- 1.0
Link to section 'Commands' of 'phg' Commands
- 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
Link to section 'Module' of 'phg' Module
You can load the modules by:
module load biocontainers
module load phg
Link to section 'Example job' of 'phg' 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 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