The Rust Programming Language

Uncovering IS-mediated discord in bacterial genomes

Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

Gemini is a modern LaTex beamerposter theme 🖼

Randomly subsample sequencing reads or alignments

Read-based phasing of genomic variants, also called haplotype assembly

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

Bioinformatics I/O libraries in Rust

Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.

Official repository for Citation Style Language (CSL) citation styles.

De Bruijn graphs in Rust

Short-read assembler for bacterial genomics based on a de Bruijn graph written in Rust 🦅

Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.

A shiny application to visualize MCscan result

💃 🌴 LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations

Rust Learning Resources

Jupyter notebooks and other resources for Think Python by Allen Downey, published by O'Reilly Media.

LaTeX source and supporting code for Think Python, 2nd edition, by Allen Downey.

Python 3 library with good support for both reading and writing VCF

liftover for python, made fast with cython

Materials for R workshop

This repository contains math tutorials I created for Bioinformatics and Computational Biology.

the pangenome graph builder

Remove human reads from a sequencing run

The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/

Antibiotic resistance prediction in minutes

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.