A fast and scalable phylogenetic tree viewer for microbiome data analysis

• UpdatedAug 4, 2024
• JavaScript

Sample search by metadata and features

• UpdatedAug 31, 2023
• Python

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

• UpdatedMar 13, 2025
• JavaScript

Assign taxonomy with blast, can be used for qiime

• UpdatedAug 18, 2023
• Python

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

• UpdatedDec 18, 2021
• Python

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

• UpdatedJul 13, 2018
• Jupyter Notebook

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

• UpdatedApr 16, 2019
• Python

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…

• UpdatedAug 14, 2018
• Perl

Docker container for running qiime

• UpdatedMay 7, 2021

Singularity Recipe for QIIME 2

• UpdatedAug 12, 2021
• Roff

Auto-q Qiime Analysis Automating Script

• UpdatedMar 24, 2022
• Python

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

• UpdatedApr 30, 2019
• R

Doctoral dissertation

• UpdatedDec 21, 2017
• TeX

Bioinformatics pipeline for analysis of diatom sequenced data

• UpdatedJul 4, 2019
• Jupyter Notebook

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

• UpdatedApr 11, 2017
• R

• UpdatedFeb 10, 2019
• Jupyter Notebook

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

• UpdatedAug 21, 2020
• Shell

QIIME2 plugin for `ili

• UpdatedOct 18, 2018
• Python

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

• UpdatedAug 10, 2018
• Python

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

• UpdatedJun 20, 2023
• Shell