Repository of the data and analysis procedures for the manuscript:
Contrasting recovery of metagenome‑assembled genomes and derived microbial communities from lizard fecal and cloacal samples Mauricio Hernández, Jorge Langa, Ostaizka Aizpurua, Yendi E. Navarro-Noya, Antton Alberdi
Data processing to generate annotated metagenome-assembled genomes and genome count tables was conducted using the following Snakemake pipeline: mg_assembly. Data analysis procedures source from the outputs of this pipeline.
The raw code used for data analysis is in the Rmd files stored in the root directory of this repository, while the bookdown-rendered webbook is available at:
alberdilab.github.io/lizard_sample_types
While the webbook provides a user-friendly overview of the procedures, analyses can be directly reproduced using the Rmd documents. Note that the code chunks that require heavy computation have been tuned off using 'eval=FALSE'. To re-render the webbook, you can use the following code:
library(bookdown)
library(htmlwidgets)
library(webshot)
render_book(input = ".", output_format = "bookdown::gitbook", output_dir = "docs")