---
title: nf-core/bytesize 29 coproID
tags: bytesize, nf-core, open-source, talk
---
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# \#29: coproID
Maxime Borry / <img src="https://openmoji.org/data/color/svg/E040.svg" width=50> @notmaxib / <img src="https://openmoji.org/data/color/svg/E045.svg" width=50> @maxibor
Max Planck Institute for Evolutionary Anthropology
---
# Overview
- What is a coprolite ? :poop:
- The challenge of identifying their source :dog: :man_and_woman_holding_hands:
- The coproID solution :computer:
- nf-core then and now
---
# What is a coprolite ?
<img src="https://upload.wikimedia.org/wikipedia/commons/thumb/f/fa/Lloydsbankcoprolite_001.jpg/1920px-Lloydsbankcoprolite_001.jpg" width=50%>
[The Lloyds bank coprolite - 9th century AD](https://hackmd.io/@aIp0E0_QTJmf9nJ0B87tfg/B1z4GjCOK)
**Coprolite ~= Paleofeces**
----
## Why do we study coprolites ?
*A window into the past on the gut microbiome and diet of historical and archaic individuals.*
For example: [blue cheese and beer consumption identified from ~ 2500 years old coprolites](https://doi.org/10.1016/j.cub.2021.09.031)
<img src="https://i.imgur.com/y1qgRPQ.png" width=20%></img>
---
# The challenge of identifying a coprolite's origin
Example: A gut microbiome study of *Elmo mupettus*
<img src="https://c.tenor.com/q1Yd0ehs3DEAAAAC/pooping-elmo.gif" width=40%></img> <img src="https://i.imgur.com/XQ8aZGy.png" width=40%></img>
----
# Archeological sample reality check
Coprolites are often found in a archeological context that can not easily help to attribute them a maker.
- No nearby human remains
- Shape/consistancy degraded
- Mixed human and animal occupation
<img src="https://i.imgur.com/L6G72ft.png" width=40%></img>
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# The coproID solution
<img src="https://dfzljdn9uc3pi.cloudfront.net/2020/9001/1/fig-2-2x.jpg" width=50%></img>
----
## Host DNA competitive mapping
**Align DNA sequencing reads simultaneously against most likely host genomes**
<a href="https://doi.org/10.1038/nmicrobiol.2016.161"><img src="https://i.imgur.com/D6j26Cu.png" width=50%></img></a>
----
## Gut microbiome profiling
Kraken2 taxonomic profiler -> Sample pairwise distance metrics -> Dimensionality reduction
<img src="https://i.imgur.com/K0CPuBd.png" width=50%></img>
----
## Predicting unknown sources from reference samples
<img src="https://i.imgur.com/eMeLOXA.png" width=50%></img>
----
## Predicting unknown sources from reference samples
<img src="https://i.imgur.com/2HJWJQo.png" width=45%></img> <a href="https://github.com/maxibor/sourcepredict"><img src="https://i.imgur.com/VZr5xuu.png" width=45%></img></a>
----
## Predicting unknown sources from reference samples
<img src="https://i.imgur.com/qU6863J.png" width=75%></img>
---
## Putting it together
Interactive report
[maximeborry.com/coproID_report.html](https://maximeborry.com/coproID_report.html)
---
# nf-core then and now
Last release of coproID in April 2020 :older_adult:
<img src="https://i.imgur.com/5nM0qcz.jpg" width=50%></img>
----
- nf-core tools v1.8
- No nf-core schema
- No DSL2/modules
Exciting to see nf-core develop so rapidly, but challenging to keep pipelines up to date.
---
# The End
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Repository: [`nf-core/coproid`](https://github.com/nf-core/coproID)
Article: [`CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content`](https://doi.org/10.7717/peerj.9001)
Slack channel: [`https://nf-co.re/join`](https://nf-co.re/join) <img src="https://cdn.brandfolder.io/5H442O3W/at/pl546j-7le8zk-6gwiyo/Slack_Mark.svg" width=7.5%></img>`#coproid`
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