Jouni Siren

bre. Spec and C library for the Binary Run-length Encoding (BRE) format

pangenome-index. C++

grlBWT. Efficient construction of the BWT using string compression

kff-cpp-api. A C++ API to read and write kff files

libbdsg. Optimized sequence graph implementations for graph genomics

libsais. The libsais library provides fast linear-time construction of suffix array (SA), generalized suffix array (GSA), longest common prefix (LCP) array, permuted LCP (PLCP) array, Burrows-Wheeler transform (BWT) and inverse BWT based on the induced sorting algorithm with optional OpenMP support for multi-core parallel construction.

GFA-spec. Graphical Fragment Assembly (GFA) Format Specification

agc. Assembled Genomes Compressor

la_vector. 🔶 Compressed bitvector/container supporting efficient random access and rank queries

PGM-index. 🏅State-of-the-art learned data structure that enables fast lookup, predecessor, range searches and updates in arrays of billions of items using orders of magnitude less space than traditional indexes

seqwish. alignment to variation graph inducer

gfakluge. A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

libhandlegraph. Library for the Handle Graph abstraction

minigraph. Sequence-to-graph mapper and graph generator

ips4o. In-place Parallel Super Scalar Samplesort (IPS⁴o)

sdsl-lite. Succinct Data Structure Library 3.0

rlzap. RLZAP: Relative Lempel-Ziv with Adaptive Pointers

DYNAMIC. Dynamic succinct/compressed data structures

libdivsufsort. A lightweight suffix-sorting library

hisat2. Graph-based alignment (Hierarchical Graph FM index)

vg. tools for working with genome variation graphs

sdsl-lite. Succinct Data Structure Library 2.0