A fast and scalable phylogenetic tree viewer for microbiome data analysis

Analysis of DNA sequencing data obtained from ancient feces of Huecoids and Saladoids, two cultures that lived in the Caribbean before the arrival of Europeans to the region.

Sample search by metadata and features

The source code for the MIND pipeline paper

Assign taxonomy with blast, can be used for qiime

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

Streamlit app forked for debugging purposes

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

Auto-q Qiime Analysis Automating Script

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

Singularity Recipe for QIIME 2

Docker container for running qiime

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

Bioinformatics pipeline for analysis of diatom sequenced data

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

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

QIIME2 plugin for `ili

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…

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