Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

🔬 Simulate microbiology scenarios and experiments.

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.

Quantitative microbial risk assessment modeling

Ecotype Simulation: Models the sequence diversity within a bacterial clade.

A computational tool for the prediction and identification of metabolites.

A repository for R code, data, figures, scripts from the manuscript "Abundance-occupancy relationships along taxonomic ranks reveal a consistency of niche differentiation in bacterioplankton with distinct lifestyles" (Submitted).

This repo contains the code and files for the linked publication

Easy-to-use tool facilitating work with Mothur.

MATLAB scripts and functions for Microbial Network Analysis (MNA)

Genomics lessons for week 4 of the Microbial Diversity course at the Marine Biological Lab in Woods Hole, MA.

Microbial community samples collected from the Trunk River in Woods Hole, MA 2014-2016.