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

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

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

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

A computational tool for the prediction and identification of metabolites.

Easy-to-use tool facilitating work with Mothur.

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

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

MATLAB scripts and functions for Microbial Network Analysis (MNA)

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

Quantitative microbial risk assessment modeling

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