Identification of ARGs and MGEs in wastewater metagenomes
This repository contains a complete pipeline for identification of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in metagenomes. It was carried out on a dedicated server in the Brazelton Lab at the University of Utah.
The batch script "utwaste-pipeline-master.sh" uses an assembly-based approach, beginning with quality control of the original sequencing reads and ending with the calculation of sequencing coverage of each predicted ARG and MGE in each metagenome.
The "plots" folder includes R code for generating plots with the tables generated by the pipeline.
https://github.com/Brazelton-Lab/seq-qc
https://github.com/Brazelton-Lab/seq-annot
https://github.com/Brazelton-Lab/lab_scripts
bbduk https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/
Megahit https://github.com/voutcn/megahit
Prodigal https://github.com/hyattpd/Prodigal
AMRFinderPlus https://github.com/ncbi/amr
CoverM https://github.com/wwood/CoverM
Bowtie2 https://github.com/BenLangmead/bowtie2
samtools https://github.com/samtools/samtools
diamond https://github.com/bbuchfink/diamond
mobileOG https://github.com/clb21565/mobileOG-db/tree/main
VFDB http://www.mgc.ac.cn/VFs/download.htm
The overall assembly-based approach, sequence coverage calculations, and the seq-qc and seq-annot packages were described in:
Thornton, CT, Tanner, W, VanDerslice, J, Brazelton, WJ (2020) Localized effect of treated wastewater effluent on the resistome of an urban watershed. GigaScience. 9 (11): giaa125, https://doi.org/10.1093/gigascience/giaa125
Brazelton WJ, McGonigle JM, Motamedi S, Pendleton HL, Twing KI, Miller BC, Lowe WJ, Hoffman AM, Prator CA, Chadwick GL, Anderson RE, Thomas E, Butterfield DA, Aquino KA, Früh-Green GL, Schrenk MO, Lang SQ. 2022. Metabolic strategies shared by basement residents of the Lost City hydrothermal field. Applied and Environmental Microbiology: e00929-22. DOI: 10.1128/aem.00929-22.
In addition, each of the tools listed above should be cited if you use them in your own work.
Brazelton lab tools were created by Christopher Thornton and Alex Hyer. Analyses of ARGs and MGEs were further developed by Robin McArdel.
This work was funded by the Centers for Disease Control through a SHEPheRD RFTOP award to Matthew Samore, Jennifer Weidhaas, and James VanDerslice (University of Utah). The point of contact for this repository is William Brazelton.