Phylogenetic ordering for million-genome microbial collections

All The Bacteria CLI — query 3.2M bacterial genomes (AMR, MLST, assemblies, metadata) from the terminal

The uncompromising Snakemake code formatter

CLI tools to access, query, and download data from AllTheBacteria database.

FISK: Fast Iteration of Spaced K-mers

Compacted and colored de Bruijn graph construction and querying

A Rust implementation of SSHash

This is the webpage of the ESGEM-AMR Working Group

Improved version of the Oxford Bioinformatics paper template

✂️🧬🧩 - rapidly identify structural variation across the bacterial ToL

Rust implementation of ntHash rolling‑hash suite, focused on contiguous k‑mer hashing for DNA sequences.

✈️ PTHash is a fast and compact minimal perfect hash function.

Ensure NEON or AVX2 is available during compilation.

Rapid k-mer matching/alignment against AllTheBacteria (r0.2, n=1.9M) on laptops within minutes/hours

Benchmark data structures for kmer sets.

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

A metagenome assembly and evaluation pipeline, focused on hi-fi long reads, but with support for lo-fi long reads and hybrid assemblies

A new high-resolution long-read metagenome assembler for even noisy reads

Fast FracMinHash sketch generator

syncmer graphs, and perhaps other sorts of sequence graphs

A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses

Implementation of the u-index

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

An efficient CLI to extract sequences from the SRA