A fast and scalable phylogenetic tree viewer for microbiome data analysis

Sample search by metadata and features

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

Assign taxonomy with blast, can be used for qiime

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Companion notebooks for "Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks"

Ultra fast program to generate publication ready taxonomic pie charts from QIIME.

Docker container for running qiime

Singularity Recipe for QIIME 2

This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequen…

Auto-q Qiime Analysis Automating Script

MSc - 16S sequence datasets, amplicon analysis, and stats

Doctoral dissertation

Bioinformatics pipeline for analysis of diatom sequenced data

A semi-automated protocol to get Qiime-formatted MaarjAM database of Arbuscular Mycorrhizal Fungi

BSc project: metagenomic analysis of urban park soil. Breakdown of some of the code I used can be viewed on this website:

QIIME2 plugin for `ili

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Bash scripts for running QIIME 1.9 and a Snakemake workflow to automate it using singularity container images.