## Metagenomics processing and analysis
This area holds our annotated processing code to facilitate following and reproducing our work in processing and analyzing the 4 metagenomes included in our manuscript: "*Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins*".
Each page notes at the top which data files are needed to pick up from that location and which programs and versions were utilized. Sequencing was performed on an Illumina MiSeq, 2x150 bps.
> The N-functional data can be interactively explored [here](https://astrobiomike.shinyapps.io/n-shiny/).
| Sample ID | Depth | # read-pairs |
|:-----:|:----:|---:|
|S1|1 mm|16,763,386|
|S2|2 mm|25,579,068|
|S3|3 mm|20,372,903|
|S4|4 mm|35,683,613|
### Table of Contents
1. [Quality filtering, co-assembly, and read-mapping](https://osf.io/9kwn3/wiki/1.%20Quality%20filtering%2C%20co-assembly%2C%20and%20read-mapping/)
2. [Integration into Anvi'o](https://osf.io/9kwn3/wiki/2.%20Integration%20into%20Anvi%27o/)
3. [Taxonomic classification](https://osf.io/9kwn3/wiki/3.%20Taxonomic%20classification/)
4. [Parsing out N-related genes and analyzing in R](https://osf.io/9kwn3/wiki/4.%20Parsing%20out%20N-related%20genes%20and%20analyzing%20in%20R/)
5. [Read-mapping to amoA genes](https://osf.io/9kwn3/wiki/5.%20Read-mapping%20to%20amoA%20genes/)
6. [Looking into K00370 and K00371](https://osf.io/9kwn3/wiki/6.%20Looking%20into%20K00370%20and%20K00371/)
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