long-read-pipelines
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broadinstitute
Long read production pipelines
Workflow filters contigs of the right lengths, identifies overlapping regions, and eventually selects contigs that represent the major haplotype based on the number of SNPs.
Following up #418 with more optimizations, and two new pipelines for ingesting single demultiplexed PacBio Hifi (u)BAM (aka a readgroup uBAM)
Project-specific.
I would like to propose the incorporation of TRGT as a special-purpose caller of tandem repeat genotypes into the PacBio CCS variant calling workflow. I have added a task and...
Summary: This Pull Request introduces several refinements to the `LongReadsContaminationEstimation` and `Contamination` workflows. The updates aim to add the `.mu`, `.UD`, and modified `.bed` resources, streamline the analysis process, reduce...
When your task is expected to run long enough, turn off preemption to save time and $. This sometimes depends on the input files' characteristics (e.g. size).
Just for testing and see how this works... Add wdls for whatshap read based phasing and shapeit5 statistical phasing pipeline. Shapeit5_v2 integrate whatshap read-based phasing results as scaffold information in...
Follow this thread https://support.terra.bio/hc/en-us/community/posts/19927348824091-Populate-workflow-documentation-area-from-Dockstore-worfklow
Mostly, update the various pacbio tools in WDL and package a docker. Carefully think about batch effects, and tracking metadata for non-trivial projects.