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BGC_class_barplot.Rmd

BGC_class_barplot.Rmd

 
 

README.md

README.md

 
 

assembly_stats.ipynb

assembly_stats.ipynb

 
 

bgc_network.ipynb

bgc_network.ipynb

 
 

bracken_self_combine.ipynb

bracken_self_combine.ipynb

 
 

ensemble_AMP_voting.Rmd

ensemble_AMP_voting.Rmd

 
 

gtdb_improvement.ipynb

gtdb_improvement.ipynb

 
 

htree.ipynb

htree.ipynb

 
 

kraken_cre.ipynb

kraken_cre.ipynb

 
 

kraken_self_single_analysis.ipynb

kraken_self_single_analysis.ipynb

 
 

maaslin2_run.ipynb

maaslin2_run.ipynb

 
 

novel612.ipynb

novel612.ipynb

 
 

rarefaction_inext_prepare.ipynb

rarefaction_inext_prepare.ipynb

 
 

rarefaction_inext_run.ipynb

rarefaction_inext_run.ipynb

 
 

reads_statistics.ipynb

reads_statistics.ipynb

 
 

scripts.Rproj

scripts.Rproj

 
 

strains_clustering.ipynb

strains_clustering.ipynb

 
 

strains_mapping.ipynb

strains_mapping.ipynb

 
 

README.md

This folder contains scripts used for the SPMP project.

Versions

Environment used to generate most of the figure can be found under envs/main.yaml. A custom graphic library (seahorse) has been used for most of the graphical output. Graphics generated here were produced based on the release alpha. R version is 4.1.0.

Link between jupyter/Rmd files and figures

F: Figure (main) SF: Supplemental figure

  • assembly_stats.ipynb: F1.A, F1.D, F1.E, SF3, F2.B
  • self_kraken_analysis.ipynb: F1.B and F1.C
  • gtdb_improvement.ipynb: F1.F and F1.G
  • rarefaction_inext_run.ipynb: F2.A
  • strains_clustering: F2.C, SF9
  • BGC_class_barplot.Rmd: F2.D
  • bgc_network.ipynb: F2.F
  • reads_statistics.ipynb: SF1 and SF2
  • bracken_self_combine.ipynb: SF4 and SF8.A
  • kraken_cre.ipynb: SF5.A
  • novel612.ipynb: SF8.B
  • ensemble_AMP_voting.Rmd: Supplementary note 2