Group B Streptococcus (GBS) identification and typing

Introduction

This workflow will identify and serotype group B Streptococcus.
This is a bioinformatic pipeline developed using WDL to perform serotyping group B Streptococcus speices. This pipeline uses docker containers which will simplyfy and reduce the installation and compatibility issues arrise duing installation of softwares. The workflow can be deployed in a standalone computer as well as using Terra platform. To run as a standalone simply clone the repository to your working environment and to run the pipeline you need a cromwell to be installed as a prerequisite. To run in Terra platform, you can use the Dockstore to search and launch to Terra.

CT-GBSIDnType workflow takes paired end reads as input, and will perform:

• Quality control
• Contamination check
• Assemble reads to scaffolds
• Confirm taxa
• Perform sequence typing (GBS)
• Check for surface genes (Pili, Alpha like proteins, Serine rich proteins)
• Check for antibiotic resistance genes

Quick Run Guide

Pipeline can be run on command line or using Terra interface.
Pre-requisite for command line: Cromwell need to be installed in the local computer

Installation

git clone https://github.com/neranjan007/GBS_Identification_and_Typing.git  

Database:

Will need the Kraken2/Bracken database present as a tar.gz file.
Standard-8 : https://benlangmead.github.io/aws-indexes/k2 : download link

Inputs

Input JSON file should have the following required input variables:

{
  "GBS_identification_n_typing_workflow.samplename": "String",
  "GBS_identification_n_typing_workflow.R1": "File",
  "GBS_identification_n_typing_workflow.R2": "File",
  "GBS_identification_n_typing_workflow.kraken2_database": "File"
} 

The pipeline expects the input files to have the standard file names produce by miseq instrument.

eg: ${samplename}_S6_L001_R1_001.fastq.gz

If the input files have any other post-fix name other than above, eg: ${samplename}_R1.fastq.gz, then the post-fix name need to be included in the input section addition to the required input varialbles.

{
  "GBS_identification_n_typing_workflow.postfix": "true",
  "GBS_identification_n_typing_workflow.read1_postfix": "_R1",
  "GBS_identification_n_typing_workflow.read2_postfix": "_R2"
}

Command line

java -jar cromwell run workflows/wf_gbs_id_and_typing.wdl -i input.json 

Reference

• Tiruvayipati, et al. "GBS-SBG - GBS Serotyping by Genome Sequencing." Microb Genom. 2021 Dec;7(12). doi: 10.1099/mgen.0.000688
• Metcalf BJ, Chochua S, Gertz RE, Hawkins PA, Ricaldi J, et al. Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA. Clin Microbiol Infect. 2017;23:574. doi: 10.1016/j.cmi.2017.02.021
• Sheppard AE, Vaughan A, Jones N, Turner P, Turner C. Capsular typing method for Streptococcus agalactiae using whole-genome sequence data. J Clin Microbiol. 2016;54:1388–1390. doi: 10.1128/JCM.03142-15
• Kapatai G, Patel D, Efstratiou A, Chalker VJ. Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences. BMC Genomics. 2017;18:429. doi: 10.1186/s12864-017-3820-5