run multiple sv evalution tools

Suffix sorting (suffix array) or L-mer Sorting Algorithm

gsufsort: building suffix arrays, LCP-arrays and BWTs for string collections [AMB 2020]

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

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

Self-contained, multi-threaded fasta/q parser

the pangenome graph builder

Personal diploid genome creation and coordinate conversion

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

Header-only library for multithreaded programming

Sparse Convolutional Denoising Autoencoders for Genotype Imputation

Inducing enhanced suffix arrays for string collections [DCC'16, TCS 2017]

Cross-platform C++11 header-only library for memory mapped file IO

Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.

genotyping by Mapping-free ALternate-allele detection of known VAriants

Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently

BigWig and BAM utilities

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Implementation of Unitigging Algorithm from "Toward Simplifying and Accurately Formulating Fragment Assembly (Myers et. al., 1995)

A standalone and lightweight C library

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A slimline C++ class for parsing command-line arguments, with an interface similar to python's class of the same name

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Genome inference from a population reference graph

Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters

A fast whole-genome aligner based on de Bruijn graphs

💥 Quickly calculate and visualize sequence coverage in alignment files

Succinct Data Structure Library 2.0