@@ -24,7 +24,7 @@ The core part of the MiMiC workflow make use of assembled metagenomic reads (e.g
### 01 - download metagenomic data public dataset
In this project, the starting point is metagenomic samples.
### 02 - Clean reads, assemble using metaspades and annotate using kraken
### 02-04 - Clean reads, assemble using metaspades and annotate using kraken
Reads are trimmed, filtered for host contamination and annotated to estimate the bacterial species composition using Kraken2<sup>6</sup>. Finally, reads are assembled using metaspades.
### 05 - Conversion of Kraken results
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@@ -46,7 +46,7 @@ The metagenomic function analysis is summarized into a table. This is repeated f
### 10 - MiMic part 3 (adjusted script)
The results of the metagenomic analysis are converted in another format. This is repeated for the bacterial isolate analysis.
###11 - MiMic part 4 (adjusted script)
###11 - MiMic part 4 (adjusted script)
Using both the metagenomic and bacterial data, calculations are performed using MiMiC functions to determine per metagenomic sample, which functions are present and how these functions can be covered by a small number of bacterial isolates. This is followed by a custom script to determine the minimal microbiome across all metagenomic samples and scripts that visualize the results.
### 12 - KEGG annotation (adjusted script)
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@@ -55,6 +55,8 @@ Using KofamScan<sup>7</sup>, gene function is translated into KEGG function.
### 13 - Visualization KEGG pathways
In order to ensure key pathways are covered in terms of function, KEGG functions are visualized side by side for both the metagenomic samples as for the minimal microbiome.
**Versioning: Version 0.1.0**
### References
1) Sergey Nurk et al., 2017 https://github.com/ablab/spades
2) Doug Hyatt et al., 2010; https://github.com/hyattpd/Prodigal
