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

An updated pipeline for pangenome investigation

IQ-TREE software version 2: phylogenetics by maximum likelihood

Fast genome-wide functional annotation through orthology assignment

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

SortMeRNA: next-generation sequence filtering and alignment tool

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

The second version of the Kraken taxonomic sequence classification system

A fast and sensitive gapped read aligner

bioBakery tools for meta'omic profiling

Publication-ready volcano plots with enhanced colouring and labeling

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

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

SPAdes Genome Assembler

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids