grep on CUDA

HGVS variant name parsing and generation with SV (structural variant) support

talk to type

Utils for streaming large files (S3, HDFS, gzip, bz2...)

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computati…

`std::execution`, the proposed C++ framework for asynchronous and parallel programming.

Google Chrome and Firefox extension that prevents the blocking of pasting into input fields

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

PBSIM3: a simulator for all types of PacBio and ONT long reads

↙️ ↘️ An R package for working with causal directed acyclic graphs (DAGs)

Plain pytorch implementation of LLaMA

Tool for parsing and converting between alternate representations of phased assemblies in GFA format

Pairing reads on genome graphs

RWKV is a RNN with transformer-level LLM performance. It can be directly trained like a GPT (parallelizable). So it's combining the best of RNN and transformer - great performance, fast inference, …

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

Index and query k-mer matrices in BGZF

minimal example implementations for bioinformatics workflow managers

Hidden Markov Model based Copy number caller

Truly parallel gzip decompression

The repository keeps the files for an IPython notebook on about how to make a simple genome assembler using python

Reference-free profiling of polyploid genomes

Scalable Bloom Filter implemented in Python

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

The ARTIC fieldbioinformatics pipeline

Wishbone is an algorithm to align cells along developmental trajectories with branches

STXXL: Standard Template Library for Extra Large Data Sets

Recurrent structural variations detection in cancer whole genomes

A team repo to client project with The Lab @ DC (GA-DSI)