SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

Extensible specification for representing and uniquely identifying biological sequence variation

Specifications of SAM/BAM and related high-throughput sequencing file formats

Conda recipes for the bioconda channel.

A Java API for high-throughput sequencing data (HTS) formats.

Scripts and files used in the generation of the COLO829 somatic SV truthset.

The second version of the Kraken taxonomic sequence classification system

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

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Updated figures for "A benchmarking of WGS-based structural variant callers" paper

Various utility tools for working with genomics data

Thousand Variant Callers Project Github Repo

Annotation of Genetic Variants

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis