ssadedin

bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

bazam

A read extraction and realignment tool for next generation sequencing data

graxxia

Wrappers for doing Mathematics in Groovy

ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing

groovy-ngs-utils

A collection of utilities for working with next generation (MPS) sequencing data in Groovy

schism

Tool for identifying novel genomic breakpoints in HTS data

seqr

beakerx

Beaker Extensions for Jupyter Notebook

beakerx_kernel_autotranslation

A repository for BeakerX Autotranslation components.

beakerx_kernel_base

Base repository for BeakerX JVM based kernels

beakerx_kernel_groovy

beakerx_tabledisplay

beakerx_tests

bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

hail-elasticsearch-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

jahmm

A Java Hidden Markov Model library

jessies

Terminator, Evergreen, lwm and friends

jsoncodegen

Groovy based generation tasks from JSON schema

koada

Front end for llama2-code-instruct

mitoreport

Intepretation software for mitochondrial variants

repo_data_020322

Some evaluation data

rnadx

rnadxview

SavvySuite

Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes

ssadedin.github.io

vrapper

Vim-like editing in Eclipse

warpy

A port of the core elements of the nf-core/wf-human-variation nanopore pipeline to bpipe

wf-human-variation