Arsenal
in Resources on Tools
This is my favorite resources’ page <!– To make life easier, we use the Markdown All in One vs-code add on You can make a shitty table first and then by Ctrl+Shift+I make it pretty Here you can find more: https://marketplace.visualstudio.com/items?itemName=yzhang.markdown-all-in-one
[NOTE] For the Copy Table button to well perform, we need to have the exact same number of buttons as the number of tables in a page. –>
TABLE OF CONTENTS
- Metabolic modeling
- Genomics and Metagenomics
- Databases
- Statistics for microbiome analysis
- My dictionary
- Visualizations
Metabolic modeling
You may have a look at this e-book 
I’ve been working on.
Genomics and Metagenomics
| Tool | Description | Documentation | Architecture | Repo | DOI | |
|---|---|---|---|---|---|---|
| skani | determining average nucleotide identity (ANI) via sparse approximate alignments | wiki | stand-alone | GitHub | OA | |
| LocalHGT | ultrafast horizontal gene transfer detection from large microbial communities | - | stand-alone | GitHub | OA | |
| gRodon | estimates maximal growth rates of prokaryotes and microbial eukaryotes from genome-wide codon usage statistics | site | R package | GitHub | original | v2 @ biorxiv |
Databases
| Resource | Description | Link | DOI |
|---|---|---|---|
| eggo | estimated growth rates from gRodon online | GitHub | OA |
Statistics for microbiome analysis
My dictionary
In the following table I describe some terms I usually read/write about.
| Term | Description |
|---|---|
| richness | number of different taxa in a community |
| evenness | the commonness or rarity of a species |
| mucin | a family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most animals |
| effective number | refers to the number of equally abundant species needed to obtain the same mean proportional species abundance as that observed in the dataset of interest (where all species may not be equally abundant) |
| copiotrophs | taxa living in environments rich in nutrients |
| succession | changes in the presence, relative abundance or absolute abundance of one or more organisms within a microbial community. Its processes can be deterministic or stochastic. Factors that drive deterministic succession fall into three categories: abiotic factors (pH, redox potential), environmental factors (cross-feeding, diet or travel) and biological factors (innate and adaptive immunity). Stochastic succession is defined as microbial community changes that are not the consequence of environmentally determined fitness (ecological drift). Whether microbial succession is more deterministic or stochastic is driven by several factors in the formation of the community, including birth mode, travel, diet (for example, human breast milk) and antibiotics. |
Visualizations
| Tool | Description | Architecture | Repo | Documentation | DOI |
| clinker | pipeline for easily generating publication-quality gene cluster comparison figures | Python package | GitHub | wiki page | OA |
