zhipengliux / spmp

Singapore Platinum Metagenomes Project

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. Note 3	ensemble_AMP_voting.Rmd