Metagen

Taxonomic analysis for 16s rRna single-end files

Usage

$ ./metagen.sh <path_to_fastQ> <ref_tax_DB>

Required Tools

The following tools are required

• FastQ Screen - Map filtered fastQ files with contaminant non-bacterial reference genomes hg19, mm10 (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
• R version 3.6.2 libraries
  • DADA2 - Standard pipeline for taxonomy assignment (https://benjjneb.github.io/dada2/tutorial.html)
  • Phyloseq - Taxonomy visualisations (https://joey711.github.io/phyloseq/index.html)
• R Data management and formatting libraries
  • Biostrings
  • ggplot2
  • ape
  • biomformat
  • readr
  • scales
  • rmarkdown
  • dplyr
  • tibble
  • treemap
  • highcharter
  • kableExtra
  • tidyr
  • plotly
  • heatmaply
• PICRUSt2 - generate functional predictions from amplicon sequences for treemap and pathway analysis (https://github.com/picrust/picrust2/wiki)

Important notes

1. The pipeline is currently designed and optimised for IonTorrent single-end data
2. Taxonomy libraries that are installed and can currently be used are:
   • Silva-v.132
   • GreenGenes-v.13_8
   • RefSeq-RDP16S_v2_May2018
3. Input fastQ file must have the naming format "subsample_sampleName.fastq". The string before the underscore will be used to declare the analysis' sample categories.
4. Output is stored in the metagen_report.html file that will be generated nside the analysis' directory

Example

$ ./metagen.sh /home/user/16_analysis_directory greengenes