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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

benchmark

A microbenchmark support library

bioparser

C++ library for parsing several formats in bioinformatics

biosoup

C++ support library for bioinformatics tools

cpecan

C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.

cpu_features

A cross platform C99 library to get cpu features at runtime.

cub

CUB is a flexible library of cooperative threadblock primitives and other utilities for CUDA kernel programming.

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

genomeworks

SDK for GPU accelerated genome assembly and analysis

googletest

Googletest - Google Testing and Mocking Framework

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

htslib

C library for high-throughput sequencing data formats

libdeflate

Heavily optimized library for DEFLATE/zlib/gzip compression and decompression

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

marginpolish

MarginPolish: Graph based assembly polishing

medaka

Sequence correction provided by ONT Research

munit

µnit is a small testing framework for C

nanocaller

Variant calling tool for long-read sequencing data

ont_sv

Identify somatic structural variations (SVs) using long read nanopore sequencing

pepper

PEPPER-Margin-DeepVariant

pybind11

Seamless operability between C++11 and Python

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

rampler

seqtk

Toolkit for processing sequences in FASTA/Q formats

simde

Implementations of SIMD instruction sets for systems which don't natively support them.

sonlib

Small general purpose library for C and Python with focus on bioinformatics.

spdlog

Fast C++ logging library.

spoa

SIMD partial order alignment tool/library

survivor

Toolset for SV simulation, comparison and filtering