GATB

compacted de Bruijn graph construction in low memory

Core library of the Genome Analysis Toolbox with de-Bruijn graph

Minia is a short-read assembler based on a de Bruijn graph

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

Short Read Connector (SRC)

GATB Minia assembly pipeline

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

k-mer counting software

Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.