Computation of average nucleotide identity with the use of MMseqs2

Fast and frugal disk based k-mer counter

Taxonomic classification of human gut viruses

A CLI tool for clustering with the Leiden algorithm

Easily and securely send things from one computer to another 🐊 📦

A tool for adding taxonomic annotations to virus contigs, mapping reads to virus genomes and much more.

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

get things from one computer to another, safely

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

Comprehensive suite for rule-based learning

All Algorithms implemented in Python

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Jaeger is a quick and precise tool for detecting phages in sequence assemblies.

📚 Freely available programming books

MMseqs2: ultra fast and sensitive search and clustering suite

genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity…

Phage-Host Interaction Search Tool

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Unix, R and python tools for genomics and data science

Applied Computational Genomics Course at UU: Spring 2020