GenomeTrakr WGS Protocol Collection and Workflow for MiSeq

DNA Extraction - Manual

Manual DNA Extraction using Qiagen DNeasy Blood and Tissue Kit

DNA Extraction - Automated

DNA Extraction from Inoculated Broth for WGS using the Maxwell RSC Cultured Cells DNA Kit

DNA Quantification

DNA Quantification using the Qubit Fluorometer

Library Preparation

Illumina DNA Prep (M) Tagmentation Library Preparation for use on an Illumina MiSeq Sequencer

Sequencing

Procedure for Operation and Maintenance of the Illumina MiSeq for Whole Genome Sequencing

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 and validating GenomeTrakr metadata templates (BioSample and SRA)

Submit sequence and metadata to NCBI:

NCBI submission protocol for microbial pathogen surveillance

Querying data at NCBI

Querying for Bacterial Pathogen Genomic Data at NCBI

Update, retract, or replace your submissions at NCBI:

NCBI Bacterial Pathogen Data Curation Protocol: SOP for Editing GenomeTrakr Submissions

Check sequence quality:

Follow the CDC's guidance for assessing QC in BioNumerics

Populate NCBI template:

***NOTE: For NCBI submission for fields not included in the BioNumerics Template, please remember to include the name of the laboratory sequencing the isolates and the surveillance effort name in the sequenced_by and project_name fields as described in Step 5 of this protocol.

Populating NCBI template for submissions using BioNumerics

Submit sequence and metadata to NCBI:

Follow the CDC's guidance for NCBI submissions through BioNumerics.

Query data at NCBI

Update, retract, or replace these records in NCBI databases, if necessary: