aeonsim

developments-in-next-generation-sequencing

Developments in next generation sequencing: instruments, read lengths, throughput. See

LDhot

Detect recombination hotspots using population genetic data.

LDhat

Estimate recombination rates from population genetic data

rtg-core

RTG Core: Software for alignment and analysis of next-gen sequencing data.

exac_browser

Browser for ExAC consortium data

circleplot

Tools for exploring distance matrices using circular plots.

Platypus

Platypus Variant Caller

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

bedtools2

bedtools - the swiss army knife for genome arithmetic

htslib

C library for high-throughput sequencing data formats

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

samtools

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

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

LICHDF_VCF_Comparer

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings