Open Overleaf/ShareLaTex projects in vscode, with full collaboration support.

A Naive Bayes classifier for metagenomic data.

Website for "Awesome Learning to Hash" https://learning2hash.github.io

Long-read mock community experiments

Some C++ code for spaced seed sketching with kmers, parallelized with OpenCilk

Application and Python module for average nucleotide identity analyses of microbes.

Approximate nearest neighbour search for microbial genomes based on hash metric

Fast Whole-Genome Similarity (ANI) Estimation

Classifier for metagenomic sequences using FM-index with run-block compressed BWT.

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

Novelty-inclusive microbial community profiling of shotgun metagenomes

Analyzing sketching and sampling approaches for fast and accurate read classification

Fast approximation of similarity for sets of very different sizes

A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.

This software calculates a confidence interval for the mutation rate from a set of observed containment indices under a simple nucleotide mutation process.

Quickly search, compare, and analyze genomic and metagenomic data sets.

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Phylogenetic orthology inference for comparative genomics

customizable pipeline to identify viral sequences from (meta)genomic data

Python3 module for running MUMmer and reading the output

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the …

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output inc…

Identifying viruses from metagenomic data by deep learning

Read Until client library for Nanopore Sequencing

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Graph-based alignment (Hierarchical Graph FM index)

C++ MapReduce Library for efficient multi-threading on single-machine

Apache Hadoop