JakeHagen

ansible_playbooks

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

bcfutils

bio2zarr

Convert bioinformatics file formats to Zarr

bix

tabix file access with golang using biogo machinery

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

docker-airflow

Docker Apache Airflow

gene_expression_norm

functions and classes to normalize gene expression count data

gtdb

remove and reattach genotypes fields from bcf

pqc

population qc - generate metrics for sanity check of large pvcfs

rnavis

incubator-airflow

Apache Airflow (Incubating)

irelate

Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang

kallisto_dock

luigi

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

luigi_pipeline

PhenoSV

PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.

PSAP_cluster

scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

slivar

variant expressions, annotation, and filtering for great good.

TS

Torrent Suite

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

vcfgo

a golang library to read, write and manipulate files in the variant call format.

vcfUtils

vcztools

Partial reimplementation of bcftools for VCF Zarr