Phylogenetic orthology inference for comparative genomics

PaCMAP: Large-scale Dimension Reduction Technique Preserving Both Global and Local Structure

Python bindings for the TaxonKit library

hybrid assembly pipeline for bacterial genomes

Reorients assembled microbial sequences

Ultra-fast preprocessing and quality control for long-read sequencing data

quality filtering tool for long reads

Tools for fast and flexible genome assembly scaffolding and improvement

Extremely fast and accurate Nanopore demultiplexing

MMseqs2 app to run on your workstation or servers

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Whole Genome Alignment Tools

base-accurate DNA sequence alignments using WFA and mashmap3

Per-base per-nucleotide depth analysis

Discovery of conserved gene clusters in multiple genomes

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

Python and Rust library for loading, saving, and manipulating taxonomic trees

Fast FASTX parsing and k-mer methods in Rust

Sequence correction provided by ONT Research

Color palette generation function using hue cycling and simple easing functions.

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Diagnostics and remedy tools for beta diversity analysis

Cloud Code for Visual Studio Code: Issues, Documentation and more

Mumemto: multi-MUM and MEM finding across pangenomes

📦BEEM-Static: An R package for inferring microbial interactions based on Lotka-Volterra models

BEEM-Static: An R package for inferring microbial interactions based on generalized Lotka-Volterra models

MetaBench is a pipeline to run and benchmark metagenomics tools. It covers database construction, taxonomic binning and profiling.