Tools and workflows by the Ruff Lab

VisuaR – R based workflow to analyze and visualize multivariate data

Ruff Lab workflow to reconstruct metagenome-assembled genomes (MAGs) from microbiomes

Create a local NCBI genome database

Map metagenomes on a genome database using BBMap

Useful tools that make life easier

Other useful tools and websites we use in our lab

Genome Taxonomy Database

PATRIC

NCBI

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Proposed standards for high-quality taxa descriptions of uncultivated Bacteria and Archaea

iTOL

ANI Calculator

MEROPS

psortb

CAZy

R plot pch symbols

Download NCBI short read archive (SRA), quality control and trimming reads using fastdump, fastqc and trimmomatic, respectively