PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species. It allows to analyze the core-genome, accessory genome and whole genome, the population structure, and the horizontal gene transfer dynamics. PATO uses, as core software, MASH , MMSeq2, Minimap2 and R.
These software can handle thousands of genomes using conventional computers
without the necessity to use on a HPC facilities. PATO can analyze data
in mash distance format (whole genome) or accnet format (accessory genome)
Most of the functions can handle both objets. Some functions are specific
for some kind of data. The primitive objet mmseq is a orthologous clustering that
is used to build accnet object, annotate the genomes and characterize
the core-, accessory- and pan-genome size (and dynamic).
PATO requires R 3.6 or newer. To install PATO package you need to install devtools package
install.packages("devtools")
You need to activate Bioconductor repository.
setRepositories()
##Then select 1 and 2.
Once you have installed devtools package and activate Bioconductor repository, type:
devtools::install_github("https://github.com/irycisBioinfo/PATO",
build_vignettes = T,
dependencies = TRUE,
repos = c("https://cloud.r-project.org/",
BiocManager::repositories()))
Some times some dependencies require system packages as libcurl. libssl or libxml2 (this example is for Ubuntu/Debian based systems):
sudo apt install libcurl4-openssl-dev libssl-dev libxml2-dev libmagick++-dev libv8-dev
Some users are experiencing problems using devtools::install_github(). If this is your case you can install the latest release from sources.
wget https://github.com/irycisBioinfo/PATO/releases/download/1.0.6/pato_1.0.6.tar.gz
R CMD INSTALL --no-multiarch --with-keep.source pato_1.0.6.tar.gz
rm pato_1.0.6.tar.gz
It could take a while because PATO has the following dependencies:
ggplot2 (>= 3.1.1),
tibble (>= 2.1.3),
htmlwidgets (>= 1.3),
htmltools (>= 0.4.0),
threejs (>= 0.3.1),
igraph (>= 1.2.4.1),
uwot (>= 0.1.3),
tidyr (>= 0.8.3),
dplyr (>= 1.0.0),
dtplyr (>= 0.0.3),
data.table (>= 1.12.2),
phangorn (>= 2.5.5),
randomcoloR (>= 1.1.0),
magrittr (>= 1.5),
Rcpp (>= 1.0.2),
mclust (>= 5.4.5),
dbscan (>= 1.1-4),
ape (>= 5.3),
parallelDist (>= 0.2.4),
foreach (>= 1.5.0),
doParallel (>= 1.0.15),
parallel (>= 3.5.2),
manipulateWidget (>= 0.10.0),
stringr (>= 1.4.0),
stringdist (>= 0.9.6),
openssl (>= 1.4.3),
Biostrings (>= 2.52.0),
microseq (>= 2.1.2)
To download the necessary databases:
library(pato)
install_db()
You can find the documentation in the wiki area