Welcome to the User Manual for the Genomics Core

The Core is part of a suite of genome analysis tools that explore bacterial genomes. The suite includes:

Application Description
The Core Genome assembly, taxonomic classification, phylogeny, annotation and mass screening.
Tool 1 Mass screening with curated databases.
Tool 2 Mass screening with genes you choose.
Tool 3 Comparison of genomes, and phylogeny.
Tool 4 Primer design: identification of unique stretches of DNA.

They are built with the pipeline manager Nextflow, and operate within Singularity containers.

The suite was developed as part of a collaborative project between Volac International Ltd. and Cardiff University, partly funded by Innovate UK as part of a knowledge transfer partnership (KTP).

What is the Core for?

The Core processes raw paired-end sequence data in order to:

  • assembly genomes (with pre- and post-quality control analysis),
  • conduct mass screening using curated libraries of genes. e.g. resfinder,
  • annotate the assembled genomes,
  • determine the taxonomic classification for each isolate, e.g. Lactobacillus plantarum,
  • draw a phylogenomic tree based on 172 common genes, and
  • reports any anomalous outcomes.

Additionally, the Core provides inputs for downstream analysis by the Tools and also for external appliances.

workflow schematic

What does the Core do?

The main components of appliance_GBA are:

  • quality and adapter trimming of raw read data by trim_galore (a wrapper for cutadapt and FastQC). FastQC runs after trimming is complete and generates a report for each sample,
  • identification of potential contamination by kraken2,
  • genomes are assembled by shovill,
  • QC is conducted on the assembled genomes using quast,
  • the assembled genomes are annotated by prokka,
  • mass screening of the assembled genomes for genes of interest or hazard by ABRicate,
  • MultiQC combines the QC and annotation reports into a single summary,
  • classification of the isolates to species level by kraken2 and fastANI. The results are combined into a single table via awk commands, and
  • LS-BSR and FastTree generate a phylogenomic tree based on 172 pre-define genes (see Zheng et al. 2015, figure 1).