GenomeTrakr WGS Protocol Collection and Workflow for MiSeq
Ruth Timme, Julie Haendiges, Maria Balkey, Tina Lusk Pfefer
Disclaimer
Abstract
Here we have created a collection of all the protocols used for WGS using the MiSeq, in order, from sample extraction to NCBI submission.
This collection has three sections:
- Section 1: WGS Wet lab workflow for Illumina MiSeq
- Section 2: Dry lab workflow for sequence QC and NCBI submission - Direct Submission
- Section 3: Dry lab workflow for sequence QC and NCBI submission - PulseNet labs
Associated protocols:
Steps
Wet lab
WGS Wet lab workflow for Illumina MiSeq
DNA Quantification
Dry lab - Direct Submission
Dry lab workflow for sequence QC and NCBI submission - Direct Submission:
The following protocols are also included in a Springer Methods book chapter collection: Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback (protocols.io)
Check sequence quality:
Quality control assessment for microbial genomes: GalaxyTrakr MicroRunQC workflow
Populate BioSample AND SRA metadata templates:
Guidance for populating GenomeTrakr metadata templates (BioSample and SRA)
Submit sequence and metadata to NCBI:
NCBI submission protocol for microbial pathogen surveillance
Update, retract, or replace these records in NCBI databases, if necessary:
NCBI data curation protocol - SOP for editing GenomeTrakr submissions (protocols.io)
Dry lab - PulseNet submission
Dry lab workflow for sequence QC and NCBI submission - PulseNet labs:
Check sequence quality:
Follow the CDC's guidance for assessing QC in BioNumerics
Populate NCBI template:
Populating NCBI template for submissions using BioNumerics v7.6
Submit sequence and metadata to NCBI:
Follow the CDC's guidance for NCBI submissions through BioNumerics.
Update, retract, or replace these records in NCBI databases, if necessary:
NCBI data curation protocol - SOP for editing GenomeTrakr submissions (protocols.io)
