monkollek

alphafold_pytorch

An implementation of the DeepMind's AlphaFold based on PyTorch for research

Arcane-Tracker

An automatic Hearthstone tracker for Android

baminfo

Tools created from htslib/samtools libraries

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

breakdancer

SV detection from paired end reads mapping

code-for-blog

Code for various tutorials and programs I've written about on my blog

firstrepo

genome_viz

Tools to produce handy genome visualizations in SVG format

HearthMirror

HSTracker

A deck tracker and deck manager for Hearthstone on macOS

htsjdk

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

htslib

C library for high-throughput sequencing data formats

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

mito_browser

JavaScript tools for exploring variant data

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

mtServerCLI

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

poretools

a toolkit for working with Oxford nanopore data

prospr

ProSPr: Protein Structure Prediction

recessiveStats

repository for analysis of recessive genes

samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

samtools

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

scissors

Split-read aligner

seqr

web-based analysis tool for rare disease genomics

tabix

Note: tabix and bgzip binaries are now part of the HTSlib project.

vcfscripts

Scripts for analyzing VCF files

verifyBamID

verifyBAMID with CRAM support