PacBio Human WGS Workflow - snakemake implementation

This repo contains a data analysis pipeline to comprehensively detect and prioritize variants in human genomes using PacBio HiFi reads. It consists of three Snakemake workflows designed to run sequentially, with PacBio HiFi BAMs or FASTQs as the primary input.

Documentation for the PacBio Human WGS Workflow (snakemake implementation) is available here.

Contributors

Juniper Lake (@juniper-lake)
William Rowell (@williamrowell)
Aaron Wenger (@amwenger)

Name		Name	Last commit message	Last commit date
Latest commit History 370 Commits
profiles		profiles
rules		rules
scripts		scripts
.gitmodules		.gitmodules
LICENSE.txt		LICENSE.txt
README.md		README.md
Tutorial.md		Tutorial.md
config.yaml		config.yaml
example_cohort.yaml		example_cohort.yaml
process_cohort.local.sh		process_cohort.local.sh
process_cohort.lsf.sh		process_cohort.lsf.sh
process_cohort.sge.sh		process_cohort.sge.sh
process_cohort.slurm.sh		process_cohort.slurm.sh
process_cohort.smk		process_cohort.smk
process_sample.local.sh		process_sample.local.sh
process_sample.lsf.sh		process_sample.lsf.sh
process_sample.sge.sh		process_sample.sge.sh
process_sample.slurm.sh		process_sample.slurm.sh
process_sample.smk		process_sample.smk
process_smrtcells.local.sh		process_smrtcells.local.sh
process_smrtcells.lsf.sh		process_smrtcells.lsf.sh
process_smrtcells.sge.sh		process_smrtcells.sge.sh
process_smrtcells.slurm.sh		process_smrtcells.slurm.sh
process_smrtcells.smk		process_smrtcells.smk
reference.yaml		reference.yaml
variables.env		variables.env

License

GenoMixer/pb-human-wgs-workflow-snakemake

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PacBio Human WGS Workflow - snakemake implementation

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