Mar 21, 2024
Version 3
GenomeTrakr WGS Protocol Collection and Workflow for MiSeq V.3
- Tina Lusk Pfefer1,
- Julie Haendiges1,
- Maria Balkey1,
- Candace Bias1,
- Ruth Timme1
- 1US Food and Drug Administration
- GenomeTrakrTech. support email: genomeTrakr@fda.hhs.gov
Protocol Citation: Tina Lusk Pfefer, Julie Haendiges, Maria Balkey, Candace Bias, Ruth Timme 2024. GenomeTrakr WGS Protocol Collection and Workflow for MiSeq. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4bwyjvo5/v3Version 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: March 19, 2024
Last Modified: March 21, 2024
Protocol Integer ID: 96944
Keywords: GenomeTrakr, whole genome sequencing, enteric pathogens, surveillance, MiSeq, genometrakr wgs protocol collection, bacterial pathogen genomic data at ncbi, bacterial pathogen genomic data, dry lab workflow for sequence qc, lab workflow for illumina miseq section, genometrakr, maxwell rsc cultured cells dna kit, workflow for miseq, sample extraction to ncbi submission, dna extraction from inoculated broth, dna extraction, dry lab workflow, lab workflow, ncbi submission, new protocol, miseq, pulsenet lab, links to protocol, illumina miseq section, added new protocol, protocol, sequence qc
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:
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.
Troubleshooting
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: Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback (protocols.io)
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 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.
Submit sequence and metadata to NCBI:
Follow the CDC's guidance for NCBI submissions through BioNumerics.
Query data at NCBI
"Querying Data at NCBI"
Update, retract, or replace these records in NCBI databases, if necessary:
Data curation protocol