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Tip revision: 86968509e38902580b04a25786c5a58ba2777b21 authored by Antonio Fernandez-Guerra on 28 February 2022, 14:31:29 UTC
Merge pull request #6 from functional-dark-side/dependabot/bundler/nokogiri-1.13.3
Merge pull request #6 from functional-dark-side/dependabot/bundler/nokogiri-1.13.3
Tip revision: 8696850
17_Cluster_DB_numbers.md
---
layout: page
title: Cluster Databases
---
<h3 class="section-heading text-primary">Environmental origin (MG)</h3>
**Starting data:**
| Data set | Samples | Sites |
|:---------:|:-------:|:-----:|
| TARA | 242 | 141 |
| Malaspina | 116 | 30 |
| OSD | 145 | 139 |
| GOS | 80 | 70 |
| HMP | 1,249 | 18 |
| Total metagenomes | 1,832 |
| ----------------- | --------------- |
| **Total ORFs** | **322,248,552** |
**MMseqs clustering:**
| | Total | Clusters ≥ 10 ORFs | Clusters 1< ORFs < 10 | Singletons |
| -------- |:-----------:|:------------------:|:---------------------:|:----------:|
| Clusters | 32,465,074 | 3,003,897 | 9,549,853 | 19,911,324 |
| ORFs | 322,248,552 | 268,467,763 | 33,869,465 | 19,911,324 |
**Cluster validation:**
| | Kept | Discarded |
| -------- | ----------- | ---------- |
| Clusters | 2,940,257 | 29,524,817 |
| ORFs | 260,142,354 | 62,106,198 |
Discarded cluster classes:
| | Singletons | Small clusters | Bad clusters |
| -------- | ---------- | -------------- | ------------ |
| Clusters | 19,911,324 | 9,549,853 | 63,640 |
| ORFs | 19,911,324 | 33,869,465 | 8,325,409 |
**Cluster and cluster community categories:**
| | K | KWP | GU | EU | Total |
| ----------- |:-----------:|:----------:|:----------:|:---------:|:---------------:|
| Communities | 24,181 | 64,938 | 146,100 | 48,095 | **283,314** |
| Clusters | 1,050,166 | 632,453 | 1,121,809 | 135,829 | **2,940,257** |
| ORFs | 172,147,128 | 30,601,694 | 54,052,275 | 3,341,257 | **260,142,354** |
<h3 class="section-heading text-primary">Environmental (MG) + Genomic origin (GTDB)</h3>
**Starting data:**
| | Genomes | Proteins |
|:---------:|:-------:|:----------:|
| Bacterial | 27,372 | 90,621,864 |
| Archaeal | 1,569 | 3,101,326 |
| Total | 28,941 | 93,723,190 |
**MMseqs incremental clustering:**
| | MG | GTDB | Total |
|:--------:|:-----------:|:----------:|:-----------:|
| Clusters | 32,465,074 | 7,958,475 | 40,423,549 |
| ORFs | 322,248,552 | 93,723,190 | 415,971,742 |
**MMseqs new clustering classes:**
| | Total | Clusters ≥ 10 ORFs | Clusters 1< ORFs < 10 | Singletons |
| -------- |:-----------:|:------------------:|:---------------------:|:----------:|
| Clusters | 40,423,549 | 3,599,944 | 11,846,082 | 24,977,524 |
| ORFs | 415,971,742 | 349,446,528 | 41,547,690 | 24,977,524 |
**Cluster validation:**
| | Kept | Discarded |
| -------- | ----------- | ---------- |
| Clusters | 5,287,759 | 35,135,790 |
| ORFs | 338,125,790 | 78,953,207 |
Discarded cluster classes:
| | Singletons | Small clusters | Bad clusters | Others** |
| -------- | ---------- | -------------- | ------------ | --------- |
| Clusters | 25,469,762 | 9,549,853 | 116,175 | 240,711 |
| ORFs | 25,469,762 | 35,579,477 | 8,902,149 | 9,001,819 |
**Others: MG clusters previously discarded cause singlentons or small clusters, which, with the integration of GTDB ORFs, became clusters with ≥ 10 ORFs. These clusters are momentaneously discarded and will be further investigated/validated.
**Cluster and cluster community categories:**
| | K | KWP | GU | EU | Total |
| ----------- |:-----------:|:----------:|:----------:|:---------:|:---------------:|
| Communities | 62,300 | 91,742 | 416,364 | 103,195 | **673,601** |
| Clusters | 1,667,510 | 768,859 | 2,647,359 | 204,031 | **5,287,759** |
| ORFs | 230,641,766 | 32,754,365 | 68,509,335 | 3,534,207 | **335,439,673** |
Summary of MG + GTDB gene cluster communites:
| Communities | K | KWP | GU | EU | Total |
| ------------- |:------:|:------:|:-------:|:-------:|:-----------:|
| MG+GTDB | 62,300 | 91,742 | 416,364 | 103,195 | **673,601** |
| only-new-GTDB | 38,119 | 26,804 | 270,264 | 55,100 | **390,287** |
| GTDB in MG | 14,241 | 20,399 | 69,204 | 2,799 | **106,643** |
| MG | 24,181 | 64,938 | 146,100 | 48,095 | **283,314** |
<h3 class="section-heading text-primary">MG + GTDB</h3>
<div class="img_container" style="width:60%; margin:2em auto;">
<img alt="MG_GTDB_venn.png" src="/img/MG_GTDB_venn.png" width="70%" height="" >
</div>
<div class="img_container" style="width:90%; margin:2em auto;">
<img alt="mg_gtdb_numbers.png" src="/img/mg_gtdb_numbers.png" width="80%" height="" >
</div>
<h3 class="section-heading text-primary">Integration with the TARA OM-RGC-v2 (OMRGC2)</h3>
OM-RGC.v2 contains 46,775,154 non-redundant genes.
**MMseqs incremental clustering:**
| | MG-GTDB | MG-GTDB-OMRGC2 | OMRGC2 | Total |
| -------- | ----------- | -------------- | --------- | ----------- |
| Clusters | 32,666,889 | 7,756,660 | 4,284,357 | 44,707,906 |
| ORFs | 158,585,789 | 297,573,606 | 6,587,501 | 462,746,896 |
**Cluster categories:**
| | K | KWP | GU | EU | Total |
| -------- |:-----------:|:----------:|:----------:|:---------:|:---------------:|
| Clusters | 1,797,860 | 829,466 | 2,853,501 | 505,933 | **5,986,760** |
| ORFs | 251,441,910 | 35,389,904 | 76,610,783 | 5,150,919 | **368,593,516** |
<div class="img_container" style="width:90%; margin:2em auto;">
**MG+GTDB+OM-RGC-v2 cluster and cluster community categories:**
| | K | KWP | GU | EU | Total |
| ----------- |:-----------:|:----------:|:----------:|:---------:|:---------------:|
| Communities | 146,665 | 140,232 | 562,330 | 291,022 | **1,140,249** |
| Clusters | 1,797,860 | 829,466 | 2,853,501 | 505,933 | **5,986,760** |
| ORFs | 251,441,910 | 35,389,904 | 76,610,783 | 5,150,919 | **368,593,516** |
</div>
<h3 class="section-heading text-primary">MG + GTDB + OMRGC2</h3>
<div class="img_container" style="width:60%; margin:2em auto;">
<img alt="MG_GTDB_OMRGC2_venn.png" src="/img/MG_GTDB_OMRGC2_venn.png" width="80%" height="" >
</div>
