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gatk-protected

GATK4 development of the license-protected part of the toolkit

gatk4

GATK4 development

gccontent-benchmark

Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)

gedmatch-tools

Tools and Python API for GEDMatch Genesis (https://genesis.gedmatch.com)

genomicsqlite

Genomics Extension for SQLite

gget

gget enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, directly into a Python or terminal programming environment. It was designed to support genomic data analysis.

glimpse

Low Coverage Calling of Genotypes

graphalignmentviewer

grizzled-scala

A general-purpose library of miscellaneous stuff for Scala.

guide-counter

gzp

Multi-threaded Compression

hap.py

Haplotype VCF comparison tools

hapcut

program for haplotype phasing from sequence reads and related tools

hapcut2

New version of hapCUT that uses a log-likelihood based approach over MEC, and is optimized for long read and other diverse NGS technologies.

hipstr

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

hisat2

Graph-based alignment (Hierarchical Graph FM index)

homebrew

The missing package manager for OS X.

homebrew-science

Scientific formulae for the Homebrew package manager

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

htsjdk

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

htslib

C library for high-throughput sequencing data formats

igv

Integrative Genomics Viewer. This is a mirror of the main repository (code.google.com/p/igv), being used for testing purposes only.

jbwa

Java Bindings (JNI) for bwa

klib

A standalone and lightweight C library

ksw

Ksw: (interactive) smith-waterman in C

ksw2

Global alignment and alignment extension

laika

Text Markup Transformer for sbt and Scala applications, transforming Markdown and reStructuredText to HTML and PDF

linguist

Language Savant. If your repository's language is being reported incorrectly, send us a pull request!

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.

magicpython

Cutting edge Python syntax highlighter for Sublime Text, Atom and Visual Studio Code. Used by GitHub to highlight your Python code!