dot plotter on top of minimap2

A repository for collecting GPU basecalling stats

syncmer graphs, and perhaps other sorts of sequence graphs

Jan is an open source alternative to ChatGPT that runs 100% offline on your computer.

CAncer Standards Long-read Evaluation

Efficient, parallel compression for terabyte-scale data

A bioinformatics tool written in Rust to find palindromic sequences in DNA

Efficient construction of the BWT using string compression

Distribute and run LLMs with a single file.

MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.

Genome mapping and spliced alignment of cDNA or amino acid sequences

Structural variant caller for real-time long-read sequencing data

Assembled Genomes Compressor

Powerful long read aligner for Ruby

DRAGEN open-source mapper

Cross-platform Rust rewrite of the GNU coreutils

PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

A fast K-mer counter for high-fidelity shotgun datasets

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment

Implicit Interval Tree with Interpolation Index

A very fast interval tree data structure

The Modular Aligner and The Modular SV Caller

A minimap2 frontend for PacBio native data formats

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

Slides for Algorithms for DNA Sequencing Coursera class

Exploration of controlled loss of quality values for compressing CRAM files