CutePeaks is a standalone Sanger trace viewer steered by a modern and user-friendly UI.

sunburst plots for taxonomy - working to update Krona

functions for analyzing phyloseq data

How to analyze shotgun metagenomic data with phyloseq - a walkthrough

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake

Code for processing amplicons associated with BioGEOTRACES cruises GA03 and GP13 prior to ingestion into CMAP

Species richness with high diversity

Network construction, analysis, and comparison for microbial compositional data

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

This is the development home of the workflow management system Snakemake. For general information, see