Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Gene cluster comparison figure generator

Tools for fast and flexible genome assembly scaffolding and improvement

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

An analysis and visualization platform for 'omics data

Eukaryotic Genome Annotation Pipeline

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Variational autoencoder for metagenomic binning

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Build a partitioned pangenome graph from microbial genomes

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

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

geNomad: Identification of mobile genetic elements

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Automatic and optimised consensus clustering of one or more heterogeneous datasets

Virus Identification By iteRative ANnoTation

fast phage annotation program

Bioinformatics program inStrain

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Pipeline for metabolic annotation of microbial genomes

Novelty-inclusive microbial community profiling of shotgun metagenomes

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

SemiBin: metagenomics binning with self-supervised deep learning

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.