Apjok-et-al-DEEPMINE-NatMicrobiol

Code deposited for paper “Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains”, Apjok et al. Nature Microbiology.

System requirements

• Apptainer/Singularity (for Illumina demultiplexing, only works on linux)
• R (for all other scripts)

Download data

Illumina reads and Nanopore contigs can be downloaded from the European Nucleotide Archive. Study Accession: PRJEB54063 (Secondary Accession: ERP138883)

suppressMessages(source("prepare_input_data.R"))

Demultiplex Illumina reads

Download Apptainer/Singularity container for demultiplexing:

# Define a local directory that will store the apptainer/singularity container
cache_dir <- "./containers"

# convert path to absolute path
cache_dir <- normalizePath(cache_dir)

# create cache directory if it doesn't already exists
if (!dir.exists(cache_dir)) {
  dir.create(cache_dir, recursive = TRUE)
}

# download container image if it is not already downloaded
if (!file.exists(paste0(cache_dir, "/mesti90-hgttree-latest.img"))) {
  cmd <- paste0(
    "singularity pull --dir ", cache_dir,
    " mesti90-hgttree-latest.img docker://mesti90/hgttree:latest"
  )
  system(cmd)
}

Demultiplex Illumina reads in first run:

setwd("./run1")
cmd <- paste0(
  "singularity exec ", cache_dir,"/mesti90-hgttree-latest.img ",
  "python3 barcode_amplicon_demux_20201026.py3"
)
system(cmd, ignore.stdout = TRUE)

Demultiplex illumina reads in second run:

setwd("./run2")
cmd <- paste0(
  "singularity exec ", cache_dir,"/mesti90-hgttree-latest.img ",
  "python3 barcode_amplicon_demux_20210201.py3"
)
system(cmd, ignore.stdout = TRUE)

Demultiplex illumina reads in third run:

setwd("./run3")
cmd <- paste0(
  "singularity exec ", cache_dir,"/mesti90-hgttree-latest.img ",
  "python3 barcode_amplicon_demux_20220505.py3"
)
system(cmd, ignore.stdout = TRUE)

Prepare supplementary table 6

setwd("./supplementary_table_6")
suppressMessages(source("Script - Supplementary table 6.R"))

Prepare supplementary table 7

setwd("./supplementary_table_7")
suppressMessages(source("Script - Supplementary table 7.R"))

Prepare supplementary table 9

setwd("./supplementary_table_9")
suppressMessages(source("Script - Supplementary table 9.R"))