Nils Homer's repositories
bfx-examples
Bioinformatics Example Repository
read-structure-examples
Example Read Structures for BAM <-> FASTQ
awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
adVNTR
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
basespace-commons
Library for use in BaseSpace apps.
COSMOS-2.0
Python Workflow and Pipeline Management System
CryptEx
Scripts used to discover and quantify non-annotated cryptic splicing in RNA-seq data
fermi-lite
Standalone C library for assembling Illumina short reads in small regions
freebayes
Bayesian haplotype-based polymorphism discovery and genotyping.
gatk-protected
GATK4 development of the license-protected part of the toolkit
grizzled-scala
A general-purpose library of miscellaneous stuff for Scala.
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
jbwa
Java Bindings (JNI) for bwa
ksw2
Global alignment and alignment extension
Laika
Text Markup Transformer for sbt and Scala applications, transforming Markdown and reStructuredText to HTML and PDF
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!
ProbHap
Probabilistic single-individual haplotyping
pyhocon-feedstock
A conda-smithy repository for pyhocon.
spoa
SIMD partial order alignment tool/library
upickle-pprint
Combined repository for uPickle/PPrint
VarDict
VarDict
VarDictJava
VarDict Java port
vcflib
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities