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# System prepended metadata

title: BRAILLE update (28-Apr-2021)
tags: [BRAILLE]

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---
tags: BRAILLE
title: BRAILLE update (28-Apr-2021)
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>**Interactive function plots and tables are [here](https://astrobiomike.shinyapps.io/braille-mg/)**.
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# BRAILLE update (28-Apr-2021)

> Previous update docs
> - [https://hackmd.io/@astrobiomike/BRAILLE-notes-31-Mar-2021](https://hackmd.io/@astrobiomike/BRAILLE-notes-31-Mar-2021)
> - [https://hackmd.io/@astrobiomike/BRAILLE-notes-17-Mar-2021](https://hackmd.io/@astrobiomike/BRAILLE-notes-17-Mar-2021)
> - [https://hackmd.io/@astrobiomike/BRAILLE-update-24-Feb-2021](https://hackmd.io/@astrobiomike/BRAILLE-update-24-Feb-2021)
> - [https://hackmd.io/@astrobiomike/BRAILLE-update-3-Feb-2021](https://hackmd.io/@astrobiomike/BRAILLE-update-3-Feb-2021)
> - [https://hackmd.io/@astrobiomike/BRAILLE-notes-12-Dec-2020](https://hackmd.io/@astrobiomike/BRAILLE-notes-12-Dec-2020)

Metagenomic processing repository with data and code is at [OSF here](https://osf.io/uhk48/wiki/home/). All data are there, but not necessarily all of the processing and figures in these note docs.

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# Summary

* Running our full workflow (assembly/gene-calling/KO annotation/taxonomy/MAG-recovery) on other relevant metagenomes for contrast
  * Running this week are Diana's 3 from Hawaii basaltic lava cave walls
    * [MA1701073](https://genome.jgi.doe.gov/portal/MA1701073metaG/MA1701073metaG.info.html) | tannish yellow ooze *biovermiculations*
    * [MA1701704](https://genome.jgi.doe.gov/portal/MA1701074metaG/MA1701074metaG.info.html) | white microbial mat
    * [GBC1701081](https://genome.jgi.doe.gov/portal/GBC1701081metaG/GBC1701081metaG.info.html) | white microbial mat
  * Ran FeGenie comparison already for these, very similar in terms of gene-copies recovered. I haven't put together the code yet to create the corresponding coverage view.

* Euks are not well represented in the metagenomic data (<1% of reads recovered). We have looked several ways now, so I feel confident it's not us just missing them in the data

* Did further MAG characterization, primarily adding in information on carbohydrate active enzymes, from the [CAZY database](http://www.cazy.org/) via [DRAM program](https://github.com/shafferm/DRAM#dram). 

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## FeGenie view with Hawaii cave metagenomes
Also added is a hypersaline microbial mat from Guerrero Negro, Mexico.

<a href="https://i.imgur.com/aRKPhv6.png"><img src="https://i.imgur.com/aRKPhv6.png"></a>

Nothing starkly different between these at this level (gene-copies recovered). I still haven't put together the code to do this with coverage. 

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## The young and the euk-less
Based on read-based also, there were barely any eukaryotic and viral sequences recovered. Kraken2 results are shown below, which uses a kmer-approach (exact matching of small stretches of nucleotides). Similar results with metaphlan3 (which uses taxon-discriminitive marker genes and read-mapping).

**Assembly-based tax coverage Domain-level**

<a href="https://i.imgur.com/Po5Yv4e.png"><img src="https://i.imgur.com/Po5Yv4e.png"></a>

**Read-based abundances Domain-level**
<a href="https://i.imgur.com/WU4o2KD.png"><img src="https://i.imgur.com/WU4o2KD.png"></a>
(~30–45% of reads classified, which is typical)

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**Assembly-based tax coverage Phylum-level**
<a href="https://i.imgur.com/xoxshGa.png"><img src="https://i.imgur.com/xoxshGa.png"></a>


**Read-based abundances Phylum-level**
<a href="https://i.imgur.com/qzVvh4H.png"><img src="https://i.imgur.com/qzVvh4H.png"></a>

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**Assembly-based tax coverage Class-level**
<a href="https://i.imgur.com/YDvcBMY.png"><img src="https://i.imgur.com/YDvcBMY.png"></a>


**Read-based abundances Class-level**
<a href="https://i.imgur.com/AlnFkZc.png"><img src="https://i.imgur.com/AlnFkZc.png"></a>

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## Carbohydrate-active enzyme MAG characterization
Adding in information on carbohydrate-active enzymes, from the [CAZY database](http://www.cazy.org/) via [DRAM program](https://github.com/shafferm/DRAM#dram). There is more the program outputs, but most are things are based on KO annotations that we already have and visualized (e.g. [here](https://hackmd.io/@astrobiomike/BRAILLE-notes-12-Dec-2020#MAG-functional-overview)). 

I haven't dug into this yet, but can see an overview interactive heatmap (snapshot below) by [clicking here](https://ndownloader.figshare.com/files/27781410).

<a href="https://i.imgur.com/WXvt2Tl.png"><img src="https://i.imgur.com/WXvt2Tl.png"></a>

[Download interactive version](https://ndownloader.figshare.com/files/27781410)