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avxtoneon

Encapsulate the frequently used AVX instructions as independent modules to reduce repeated development workload.

badread

a long read simulator that can imitate many types of read problems

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cactus

Official home of genome aligner based upon notion of Cactus graphs

colord

A versatile compressor of third generation sequencing reads.

concurrentqueue

A fast multi-producer, multi-consumer lock-free concurrent queue for C++11

gbwt

Substring index for paths in a graph

graphaligner

hmm

Hidden Markov Model

kraken2

The second version of the Kraken taxonomic sequence classification system

minigraph

Sequence-to-graph mapper and graph generator

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

nanosim

Nanopore sequence read simulator

oi-public-library

OI essays and learning materials

pbwt

Implementation of Positional Burrows-Wheeler Transform for genetic data

vg

tools for working with genome variation graphs

xxhash

Extremely fast non-cryptographic hash algorithm

zlib

A massively spiffy yet delicately unobtrusive compression library.