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Bioinformatics Pipelines and Visualization
Inception: April 2020
# of Members: 60+
Chairs
Gültekin Ünal
Ankara University, Türkiye
Emily Smith
Theiagen Genomics, USA
Victoria Dyster
Mitra Bio, UK
Contact: [email protected]
Emeritus
Jamie Southgate
Kevin Libuit
Our Working Group is focused on the establishment of standards and best practices for bioinformatic pipeline development, workflow templating and management, packaging and containerization, code and documentation standards and strategies for support. Well integrated visualization and reporting tools are critical to convey actionable information to a range of stakeholders and decision-makers across multidisciplinary public health teams.
Virtual meetings are held bi-monthly on Thursdays, with further sub-working group meetings taking place at various times during the month. be used. New members that have signed up are invited to join in the discussions and can participate in volunteering their time on any one of the sub-working group projects:
In an attempt to assist this integration process, the bioinformatics pipeline and visualization working group of the Public Health Alliance for Genomic Epidemiology (PHA4GE) has drafted this living document to help define the major bioinformatics challenges for SC2 genomic analysis and suggest various open-source and freely available bioinformatics resources to address them.
The PHA4GE Pipelines and Visualization Working Group has created this document to highlight critical open-source/accesses resources to aid in the understanding and further analysis of the Omicron variant.
SARS-CoV-2 recombinants have garnered the attention of the public health community largely due to the unknown clinical and epidemiological implications. This uncertainty emphasizes the need to detect and characterize recombinant SARS-CoV-2 genomes, but the ability to do so rapidly and systematically is not without challenges.
In an attempt to assist with quality control (QC) measures, the bioinformatics pipeline and visualization working group of the Public Health Alliance for Genomic Epidemiology (PHA4GE) has drafted this living document to help define the QC challenges for SC2 genomic analysis and suggest a QC systems solutions to address them.
Genomic analysis of Mpox virus (MPXV) samples by public health laboratories is a critical component in understanding the global outbreak. The integration and awareness of appropriate bioinformatics tools to support these endeavours are potential challenges.
The proposed standards aim to provide a guidance framework for development, testing, maintenance of bioinformatics software. By adhering closely to these standards, software developers can enhance the quality, reliability and sustainability of their software, facilitating impact in public health research.
Public Health Agency of Canada
Global Health and Infectious Diseases Control Institute
Ekiti State Teaching Service Commission
EMBL-EBI
SIB Swiss Institute of Bioinformatics
Aga Khan University Hospital
University of Nairobi (CEBIB)
Washington State Department of Health
Uganda National Health Laboratories and Diagnostic
Institut Pasteur Dakar
Public Health Wales
National Reference Center for Genomics, Sequencing and Bioinformatics
Massachusetts Department of Public Health
University of Antwerp
Galaxy Project
National Center for Biotechnology Information
Ministry of Health
South African Medical Research Council
Centre for Biomedical Research Initiatives
Armauer Hansen Research Institute
All India Institute of Medical Sciences, New Delhi
Biodefense and Public Health Group at LANL
New England Biolabs
University of Nairobi
WRAIR
University of Edinburgh
South African Medical Research Council
Universidad de La Laguna
University of Liverpool
Kumasi Center for Collaborative Research in Tropical Medicine
SENASICA
Makerere University
Broad Institute of MIT and Harvard
National Service of Health, Safety and Agrifood Quality
Kumasi Center for Collaborative Research in Tropical Medicine
Theiagen Genomics
PathWest Laboratory Medicine
National Malaria Elimination Centre, Lusaka, Zambia; Malaria Control & Elimination Partnership for Africa
Broad Institute
Helix Biogen Institute
Federal University of Technology, Akure
Translational Genomics Research Institute (TGen)
University of Oxford / Wellcome Sanger Institute
Ethiopian Public Health Institute
Reference Central Laboratory
Gujarat University, Ahmedabad
US CDC
Scripps Research
World Health Organization
US CDC
Instituto de Salud Carlos III (ISCIII)
Theiagen Genomics
Swiss TPH
Theiagen Genomics
Research Institute
Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP)
WACCBIP, University of Ghana
University of South Dakota
University of Oxford
Laboratorio Central de Salud Pública
Institut Pasteur de Tunis
Higher institute of Biotechnology of Monastir
Theiagen Genomics
Public Health Agency of Canada / University of Manitoba
Africa CDC
Makerere University
University College Dublin
National Virology Reference laboratory of Turkey
US CDC
National Institute of Applied Sciences and Technology
Institute of Human Virology
Aga Khan University
UKHSA / Imperial College London
APHL / US CDC
Institute of Health Carlos III
Makerere University
Kumasi Centre for Collaborative Research into Tropical Medicine
Kwame Nkrumah University of Science and Technology
PHA4GE
US CDC
Wayne State University
Texas Children's Hospital, Baylor College of Medicine
Public Health Ontario
Ohio Department of Health / CDC Foundation
US CDC
University of Lisbon
Institute of Environmental Science and Research Limited (ESR)
ILRI CGIAR
Institute of Technology and Renewable Energy (ITER)
Scripps Research
National Microbiology Laboratory Branch, Public Health
Bernard-Nocht Institute for Tropical Medecine
LCSP-MSPBS
University of Liverpool
Wellcome Sanger Institute
Chan Zuckerberg Initiative
Theiagen Genomics
University of Botswana
Noguchi Memorial Institute for Medical Research
National Public Health Laboratory
Universitas Airlangga
Statens Serum Institut
BHSCT Regional Virology Laboratory
Universidade Católica do Paraná (PUCPR)
The Pennsylvania State University
University of Melbourne
Pwani University, Kilifi
NIH
State Department of Public Health
Scripps Research
Government Agency
Theiagen Genomics
Pwani University
University of California, Merced
DPHL
Copperbelt University
National Institute for Communicable Diseases
Instituto de Medicina Molecular João Lobo Antunes
EMBL-EBI
Pwani University
University of Birmingham
University of Cape Town
University of Dhaka
National Institute for Communicable Diseases
Université Abdelmalek Essaadi
Nigerian Institute of Medical Research
Instituto Nacional de Salud
Makerere University
University of Cape Town
SANBI
University of Liverpool
Chan Zuckerberg initiative
Institute of Tropical Medicine
Kathmandu University Hospital
University of Basel
National institute for Communicable Diseases
Wyoming Public Health Laboratory
United States Food and Drug Administration
Makerere University
Yale School of Public Health / SalivaDirect Inc.
Pennsylvania Department of Health
The Aga Khan University Hospital
Institute of Health Carlos III
Public Health Wales
NIH / USDA
Public Health Research Institute
National Institute for Communicable Diseases
Botswana Harvard AIDS Institute Partnership
Sorbonne University
Bill and Melinda Gates Foundation
University of Bristol
JIPMER
Washington State Department of Health
Wellcome Sanger Institute
The Central Public Health Laboratories
Tribhuvan University
University of Cape Town
Kumasi Center For Collaborative Research In Tropical Medicine
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PathWest Laboratory Medicine
Centre de recherche et de formation en infectiologie de Guinée (CERFIG)
Cardiff University
University of Melbourne
University of Washington
South African Research Council
Institute of Human Virology
Mitra Bio
UAntwerp
Centre Pasteur du Cameroun
Aga Khan University Medical College
Noguchi Memorial Institute for Medical Research
Galaxy Europe / University of Freiburg
Botswana-Harvard AIDS Institute Partnership
China National Center for Bioinformation
University of Bath
Global One Health Initiative (GOHi) Ohio State University
NCDC
National University of Sciences & Technology (NUST)
CDC
Medical Biology Department
Ohio Department of Health
R4DHP
Delaware Division of Public Health
US CDC
University of Yaoundé I
Private Industry
MRC / UVRI / LSHTM / Makerere university
KEMRI | Wellcome Trust Research Program
University Of Ibadan
Rhodes University
University College London
University of Virginia
Gujarat Biotechnology Research Centre
Lugar Research Center
University of Virginia
Noguchi Memorial Institute for Medical Research
University of Pretoria
Institute of Human Virology
Noguchi Memorial Institute for Medical Research
Chulalongkorn University
Institute for Medical Research, National Institute of Health
Animal Health Diagnostic Center - Cornell University
SA Pathology
Research institute
Chulalongkorn University
Georgia Tech Research Institute
Federal University of Rio de Janeiro
Mohammed VI Polytechnic University
Michigan State University
ARTPARK, Indian Institute of Science
Queensland health
ARTPARK, Indian Institute of Science
University of Freiburg Medical Centre
KEMRI
State Government
Deakin University
University of Glasgow
University of Michigan
International Center for Research and Training in Applied Genomics and Health Surveillance (CIGASS)
Government
Ghana Institute of Management and Public Administration
University of Oxford
Simon Fraser University
SANBI
Zihi Institute
University of California San Diego
Opendream
Tshwane University of Technology
World TB Day is observed on March 24 each year to raise public awareness and understanding about one of the world’s deadliest infectious killers
We are thrilled to announce a PHA4GE Bioinformatics Pipelines and Visualizations Working Group Webinar, featuring a talk by Kevin Libuit from Theiagen Genomics. Kevin shares the progress made by the working group on "Best Practices for Public Health Bioinformatics Pipelines".
Amidst an atmosphere charged with anticipation and excitement, the first day of the PHA4GE Conference burst onto the scene, igniting minds and sparking conversations that promised to shape the future of pathogen genomics, globally.