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

The ARTIC fieldbioinformatics pipeline

Reference-free profiling of polyploid genomes

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

talk to type

Hidden Markov Model based Copy number caller

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

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

Python package and routines for merging SV VCF files

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…

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

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

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

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

Pairing reads on genome graphs

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

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, …

grep on CUDA

Plain pytorch implementation of LLaMA

Scalable Bloom Filter implemented in Python

Dot: An interactive dot plot viewer for comparative genomics

minimal example implementations for bioinformatics workflow managers

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

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

Truly parallel gzip decompression

Fast and frugal disk based k-mer counter

STXXL: Standard Template Library for Extra Large Data Sets

A tuning dictionary available to use in FoxDot