Sampling CPU and HEAP profiler for Java featuring AsyncGetCallTrace + perf_events

tools for working with genome variation graphs

Accelerated BLAST compatible local sequence aligner.

🔬 Assemble large genomes using short reads

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Fast and frugal disk based k-mer counter

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Kraken taxonomic sequence classification system

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

modular k-mer count matrix and Bloom filter construction for large read collections

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

Index kmtricks bf matrices

Fast and compact locality-preserving minimal perfect hashing for k-mer sets.

De Bruijn graph representation in low memory

An integrated high performance bioinformatics toolkit

toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files

parallel algorithms for small hitting set approximations

A toolkit for de novo genome assembly based on Pregel.

kProcessor: kmers processing framework.