Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Workflow Description Language developer tools & local runner

A battery of methylation tools for PacBio HiFi reads

Convert bioinformatics file formats to Zarr

bcftools-compatible querying and format conversion for VCF Zarr

Python drop-in replacement for PyHPO using Rust

This is a dev-to-production repo for the Kids First Long reads pipeline

Long read production pipelines

Scalable gVCF merging and joint variant calling

Tools (written in C using htslib) for manipulating next-generation sequencing data

C library for high-throughput sequencing data formats

xSqueezeIt VCF/BCF Genotype data compressor with extensible compute friendly format

An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data