Nils Homer's Projects
GATK4 development of the license-protected part of the toolkit
GATK4 development
Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)
Tools and Python API for GEDMatch Genesis (https://genesis.gedmatch.com)
Genomics Extension for SQLite
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.
Low Coverage Calling of Genotypes
A general-purpose library of miscellaneous stuff for Scala.
Multi-threaded Compression
Haplotype VCF comparison tools
program for haplotype phasing from sequence reads and related tools
New version of hapCUT that uses a log-likelihood based approach over MEC, and is optimized for long read and other diverse NGS technologies.
Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
Graph-based alignment (Hierarchical Graph FM index)
The missing package manager for OS X.
Scientific formulae for the Homebrew package manager
Specifications of SAM/BAM and related high-throughput sequencing file formats
A Java API for high-throughput sequencing data (HTS) formats.
C library for high-throughput sequencing data formats
Integrative Genomics Viewer. This is a mirror of the main repository (code.google.com/p/igv), being used for testing purposes only.
Java Bindings (JNI) for bwa
A standalone and lightweight C library
Ksw: (interactive) smith-waterman in C
Global alignment and alignment extension
Text Markup Transformer for sbt and Scala applications, transforming Markdown and reStructuredText to HTML and PDF
Language Savant. If your repository's language is being reported incorrectly, send us a pull request!
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.
Cutting edge Python syntax highlighter for Sublime Text, Atom and Visual Studio Code. Used by GitHub to highlight your Python code!