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budgies icon budgies

This repository contains code for reproducing the results from Cooke et al 2017

gatk-protected icon gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

gbstools icon gbstools

Bioinformatics tools for reduced representation sequencing data

germline icon germline

Linear time detection of Identity by Descent

graal icon graal

Software from Marie-Nelly et al., 2014 (High-quality genome assembly using chromosomal contact data)

halplot icon halplot

A program for plotting HAL (hierarchical alignment format) graphs

jobtree icon jobtree

Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.

lachesis icon lachesis

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

progressivecactus icon progressivecactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

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