Data and scripts for reproducing the analyses in the SPMP project

This repository contains data and scripts used for our Singapore Platinum Metagenomes Project (SPMP) study.

Directory structure

• envs: Conda environment used for this project
• scripts: folder containing code used for this project (jupyter and Rmarkdown)
• tables: Input data used

Software versions

Python - jupyter and R version 4.1.0 with tidyverse version 1.3.1

Unusual library

Most of the figure has been generated using seahorse, a custom plotting library based on seaborn.

Raw data availability

• Raw sequencing data has been uploaded to European Nucleotide Archive
• Assemblies and annotations will be available at Figshare

Citation

Please cite our manuscript on Nature communication.

Contact

Please direct any questions or feedback to Jean-Sebastien Gounot and Niranjan Nagarajan.

Figures to script relationship

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