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bcftools

bcftools_plugins

bgt

Flexible genotype query among 30,000+ samples whole-genome

bgzeof

Detect truncation of BGZF files by checking the EOF marker exists

biogenomics-2017-vgp-poster

Plans for scaling vertebrate genome sequencing and assembly at the Sanger Institute

bog_2015_poster

64,976 whole genome haplotypes from the Haplotype Reference Consortium and efficient algorithms to use them

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

capmq

Simple program to cap mapping quality in a given alignment file

crumble

Exploration of controlled loss of quality values for compressing CRAM files

dazz_db

The Dazzler Data Base

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

gi2017-vgp-poster

Scaling up reference quality assembly of vertebrate genomes

hapdip

The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data

hrc-release1

Setup for genotype likelihood calculation for the Haplotype Reference Consortium Release 1

htslib

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

minimap2

A fast pairwise aligner for genomic and spliced nucleotide sequences

pbwt

phd_thesis

samtools

sga

tabix

vg

tools for working with variant graphs

vgp-assembly

VGP repository for the genome assembly working group

vgp.github.io

www.htslib.org

The http://www.htslib.org/ web site