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.

LLM inference in C/C++

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

Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

DCNet — Denoising (DNA) Sequence With a LSTM-RNN and PyTorch & Neural DBG

A demo of the Python C API for CodeMonkeys

A fast and sensitive gapped read aligner

Near-optimal RNA-Seq quantification

Tools for working with SAM/BAM data