Tools for phylogenetic data analysis including visualization and cluster-computing support.
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Updated
Aug 10, 2018 - Python
Tools for phylogenetic data analysis including visualization and cluster-computing support.
A repository containing a demo microbiome workflow for R and Python
Bash scripts for running QIIME 1.9 and a Snakemake workflow to automate it using singularity container images.
Streamlit app forked for debugging purposes
Tutorials on microbiome analysis using the Quantitative Insights Into Microbial Ecology (QIIME) platform
The source code for the MIND pipeline paper
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.
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
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…
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