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Simple re-analysis of mackerel and seawater marker gene sequencing samples in QIIME 2 + Songbird + Qurro

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knightlab-analyses/qurro-mackerel-analysis

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qurro-mackerel-analysis

What is this repository?

This main Jupyter notebook in this repository (Mackerel 16S Data Analysis.ipynb) performs a simple re-analysis of mackerel and environmental sample 16S data (Qiita study ID 11721, and described in Minich et al. 2019) in QIIME 2, Songbird, and Qurro. This is for the Qurro manuscript (now available in NAR Genomics and Bioinformatics here).

There are some other notebooks and files in this repository that were used in the process of preparing the manuscript, also. Here I'll try to explain some of these.

Jupyter Notebooks

We recommend using nbviewer to view the notebooks in this repository:

About the input/ folder

This folder contains the input data for this analysis notebook (note that SILVA database files are not included; as the notebook describes, you'll have to download those yourself if you want to rerun this analysis). This input data should match the data on Qiita for this study, at least as of November 10, 2019.

About the output/ folder

This folder contains most of the output from the main notebook (Mackerel 16S Data Analysis.ipynb).

As you can see from this repository's .gitignore file, files in his directory with names matching the pattern silva*.qza are not included; this is because most of these files are pretty large, and GitHub yelled at me when I tried to commit them to this repository (so I had to do this and remove these files from the repository + repository history).

Viewing these artifacts/visualizations

You can view all of the QIIME 2 artifact/visualization files here in q2view by providing a URL of the format https://raw.githubusercontent.com/knightlab-analyses/qurro-mackerel-analysis/master/output/songbird-regression-summary.qzv, where you can replace songbird-regression-summary.qzv with whatever the QZA/QZV file you want to view is named.

Here are some links that'll take you straight to q2view:

About the figures/ folder

Please see the README in this folder describing the Qurro paper's figures. The script mentioned in the implementation section (for editing Vega-Lite specifications to make text bigger, etc.) is available in this folder as biggify.py.

Why did you make this README so long?

Hey, it's not that long!

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Simple re-analysis of mackerel and seawater marker gene sequencing samples in QIIME 2 + Songbird + Qurro

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