Trends In Prokaryote Genomics

R script for identifying trends in bacterial and archaeal genomics through number of genome sequencing projects submitted to ncbi per year.

Dependencies

• ggplot2
• stringr
• tidyr
• tidyverse
• data.table

Installing dependencies

install.packages(c("stringr,ggplot2,tidyr,tidyverse,data.table"))

Steps

• Data gathering from the ncbi ftp repository (ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt)

• Data formatting: leave only genera and years

• Function (subsetting and plotting)

Example outputs

Human pathogens

genomic_trends("Escherichia|Pseudomonas|Vibrio|Campylobacter|Salmonella|Brucella", 3)

Some archaea

genomic_trends("Methanosarcina|Ignicoccus|Pyrococcus|Sulfolobus", 2)

Credits

Manuel García-Ulloa (https://github.com/manuelgug)
Mariette Viladomat Jasso (https://github.com/MarietteViladomat)