Miscellaneous "recipes" for the Conda packaging system.

Recommended Graphtyper pipelines

A small set of test cases for long-read assembly tools

Make PCAWG consensus calls given input VCFs

Data for the first few shell genomics workshop lessons from Data Carpentry

An example of baking a static linked linux binary into a container alone with nothing else

A CWL version of the Seqware OxoG workflow. This repository also contains scripts and dockerfiles used by the stand-alone versions of these components.

GoingViral is a pipeline for the analysis of SISPA generated viral metagonomics reads. It's a configurable pipeline that performs multiple functions to generate clean viral metagenomics reads that …

An c++ implementation of the LSD algorithm to detect super bubbles

Scripts for studying SVs via graphs constructed from whole-genome-alignment

Benchmarking of htslib and other tools

scripts for interpreting GFAs made by the shasta assembler

A dockstore tool containing variantbam, intended for use as a part of the Dockstore OxoG workflow

Code for calling de novo mutations in Chernobyl trios.

talk to type

Set up GISTIC2 workflow (no marker file required)

Pipeline to run sequenza from start to finish either from BAM or mpileup