This repository contains data and scripts used for our Singapore Platinum Metagenomes Project (SPMP) study.
- envs: Conda environment used for this project
- scripts: folder containing code used for this project (jupyter and Rmarkdown)
- tables: Input data used
Python - jupyter and R version 4.1.0 with tidyverse version 1.3.1
Most of the figure has been generated using seahorse, a custom plotting library based on seaborn.
- Raw sequencing data has been uploaded to European Nucleotide Archive
- Assemblies and annotations will be available at Figshare
Please cite our manuscript on Nature communication.
Please direct any questions or feedback to Jean-Sebastien Gounot and Niranjan Nagarajan.
| Figure title | Script file |
|---|---|
| Figure 1.A | assembly_stats.ipynb |
| Figure 1.B left | kraken_self_single_analysis.ipynb |
| Figure 1.B right | kraken_self_single_analysis.ipynb |
| Figure 1.C | kraken_self_single_analysis.ipynb |
| Figure 1.D | assembly_stats.ipynb |
| Figure 1.E | assembly_stats.ipynb |
| Figure 1.F | gtdb_improvement.ipynb |
| Figure 1.G | gtdb_improvement.ipynb |
| Figure 2.A | rarefaction_inext_run.ipynb |
| Figure 2.B | assembly_stats.ipynb |
| Figure 2.C | strains_clustering.ipynb |
| Figure 2.D | BGC_class_barplot.Rmd |
| Figure 2.E | Schematic representation |
| Figure 2.F | |
| S. Figure 1 | reads_statistics.ipynb |
| S. Figure 2.A | reads_statistics.ipynb |
| S. Figure 2.B | reads_statistics.ipynb |
| S. Figure 3 | kraken_self_single_analysis.ipynb |
| S. Figure 4 | kraken_self_single_analysis.ipynb |
| S. Figure 5.A | assembly_stats.ipynb |
| S. Figure 5.B | assembly_stats.ipynb |
| S. Figure 6.A | assembly_stats.ipynb |
| S. Figure 6.B | assembly_stats.ipynb |
| S. Figure 7 | bracken_self_combine.ipynb |
| S. Figure 8.A | kraken_cre.ipynb |
| S. Figure 8.B | strains_mapping.ipynb |
| S. Figure 9 | Schematic representation |
| S. Figure 10.A | assembly_stats.ipynb |
| S. Figure 10.B | assembly_stats.ipynb |
| S. Figure 11.A | bracken_self_combine.ipynb |
| S. Figure 11.B | novel612.ipynb |
| S. Figure 12.A | strains_clustering.ipynb |
| S. Figure 12.B | strains_clustering.ipynb |
| S. Figure 13 | BGC_class_barplot.Rmd |
| S. Figure 14 | BGC_class_barplot.Rmd |
| S. Figure 15 | ensemble_AMP_voting.Rmd |