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af_analysis

Analysis scripts for 30x vs 15x HiSeq X WGS analysis

agp_tools

Set of tools for working with scaffolds and AGP files

auto_qc_mkii

Prototype for a non-VRPipe way of running auto-ac

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bionanoanalyst

BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.

blasr

BLASR: The PacBio® long read aligner

bwa

Burrow-Wheeler Aligner

bwa-mem2

MP15's private working fork of bwa-mem2

codecarbon

mp15's working fork of codecarbon for Pull requests etc.

dng_dev

Martin's dev repo for DeNovoGear, expect rebases. A program to detect denovo-variants using next-generation sequencing data. (http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html)

dorado

Oxford Nanopore's Basecaller (mp15 working copy)

droidbattles

A programming game, where you program bots in assembly.

falcon

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

falcon_unzip

Making diploid assembly becomes common practice for genomic study

fastq-screen

(working copy) Detecting contamination in NGS data and multi-species analysis

fermi2

genomicsbench

A benchmark suite to study the performance characteristics of genomics applications

ggtree

a phylogenetic :palm_tree: viewer for different types of :evergreen_tree: annotations

graviton-builder

CDK builder for building graviton hosts for the benchmark suite

hapdup

Pipeline to convert a haploid assembly into diploid (working copy)

hiseq_x_variant_evaluation

Paper in preparation for work on evaluating calling on the Illumina HiSeq X

hla_db_util

Utilities for making sense of the IMGT/HLA database

hts-specs

MP15's working changes to the specifications of SAM/BAM and related high-throughput sequencing file formats

htsjdk

Private working repo for htsjdk

htslib

C library for high-throughput sequencing data formats (MP15 private repo)

irods

Open Source Data Management Software

m3-avionics

Martlet 3 Avionics

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mp15.github.io

nf-core_configs

working fork of NF cores Config files used to define parameters specific to compute environments at different Institutions