Apr 28, 2026
Version 6
GenomeTrakr WGS Protocol Collection and Workflow for MiSeq V.6
- Tina Pfefer1,
- Julie Haendiges1,
- Maria Balkey1,
- Candace Bias1,
- Ruth Timme1
- 1US Food and Drug Administration
- GenomeTrakrTech. support email: [email protected]
Protocol Citation: Tina Pfefer, Julie Haendiges, Maria Balkey, Candace Bias, Ruth Timme 2026. GenomeTrakr WGS Protocol Collection and Workflow for MiSeq. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4bwyjvo5/v6Version created by Tina Pfefer
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 28, 2026
Last Modified: April 28, 2026
Protocol Integer ID: 315885
Keywords: GenomeTrakr, whole genome sequencing, enteric pathogens, surveillance, MiSeq, genometrakr wgs protocol collection, bacterial pathogen genomic data at ncbi, dry lab workflow for sequence qc, sample extraction to ncbi submission, bacterial pathogen genomic data, metadata templates for ncbi submission, lab workflow for illumina miseq section, genometrakr, workflow for miseq, ncbi submission, ncbi template for submission, maxwell rsc cultured cells dna kit, dna extraction from inoculated broth, pulsenet lab, links to protocol, new protocol, added new protocol, removed protocol, populating ncbi template, dna extraction, dry lab workflow, lab workflow, protocol, using pulsenet, miseq, ncbi, sequence qc, using bionumeric, illumina miseq section, pathogen
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
Version history:
V6:
Steps 15 and 16 - Direct links added for protocols referenced in these steps.
V5:
Links to protocols updated with latest version
V4:
- Links to protocols updated with latest version, and
- Step 13 - Removed protocol "Populating NCBI template for submissions using BioNumerics", and replaced with protocol "Populating metadata templates for NCBI submissions using PulseNet 2.0"
V3:
- Links to protocols updated with latest version,
- Added new protocol: DNA Extraction from Inoculated Broth for WGS using the Maxwell RSC Cultured Cells DNA Kit,
- Added new protocol: Querying for Bacterial Pathogen Genomic Data at NCBI.
WGS Wet Lab Workflow for Illumina MiSeq
DNA Extraction - Manual
DNA Extraction - Automated
Protocol
CREATED BY
Julie Haendiges
DNA Quantification
Library Preparation
Protocol
CREATED BY
Julie Haendiges
Sequencing
Protocol
CREATED BY
Julie Haendiges
Dry Lab Workflow for Sequence QC and NCBI Submission - Direct Submission
The following protocols are also included in a Springer Methods book chapter collection:
Check sequence quality:
Protocol
CREATED BY
Ruth Timme
Populate BioSample AND SRA metadata templates:
Protocol
CREATED BY
Ruth Timme
Submit sequence and metadata to NCBI:
Querying data at NCBI
Update, retract, or replace your submissions at NCBI:
Protocol
CREATED BY
Ruth Timme
Dry Lab Workflow for Sequence QC and NCBI Submission - PulseNet Labs
Check sequence quality:
Follow the CDC's guidance for assessing QC in PulseNet 2.0
Populate NCBI template:
Protocol
CREATED BY
Maria Balkey
Submit sequence and metadata to NCBI:
Follow the CDC's guidance for NCBI submissions through PulseNet 2.0.
Query data at NCBI
Update, retract, or replace these records in NCBI databases, if necessary:
Protocol
CREATED BY
Ruth Timme