BitMagic Library

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

RAxML Next Generation: faster, easier-to-use and more flexible

Bayesian haplotype-based mutation calling

A Toolkit for Programming Parallel Algorithms on Shared-Memory Multicore Machines

Library code for programming contests

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Fast and frugal disk based k-mer counter

Bloom-filter based minimal perfect hash function library

Genome browser and variant annotation

de novo sequence assembler using string graphs

This repository is a fork of Microsoft Research's homomorphic encryption implementation, the Simple Encrypted Arithmetic Library (SEAL). This code wraps the SEAL build in a docker container and pro…

Fast and accurate gene fusion detection from RNA-Seq data

The study & production material for https://www.youtube.com/watch?v=Pc8DfEyAxzg

base-accurate DNA sequence alignments using WFA and mashmap2

A gap-closing software tool that uses long reads to enhance genome assembly.

Population-scale genotyping using pangenome graphs

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It u…

Genomics Extension for SQLite

Code examples of fast and simple k-mer counters for tutorial purposes

SIMD partial order alignment tool/library

Assembled Genomes Compressor

SMC++ infers population history from whole-genome sequence data.

Graph realignment tools for structural variants

alignment to variation graph inducer

Scalable gVCF merging and joint variant calling for population sequencing projects

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

microsatellite instability detection using tumor only or paired tumor-normal data