Bacterial Comparative Genomics

Virtual Workshop

Bacterial Comparative Genomics

Prior knowledge of Linux, genomics and bioinformatics concepts is recommended.

Skills you will gain:

Data Handling and Quality Control

Genome Assembly

Genome Annotation

Antimicrobial Resistance Analysis

About Workshop

Explore the intricacies of bacterial genomics in our Advanced Workshop on Bacterial Comparative Genomics. Designed for higher education audiences, this virtual workshop provides an immersive experience into the analysis of bacterial genomes using cutting-edge bioinformatics tools and techniques. Over three intensive days, participants will gain practical skills in processing read data, performing de novo assembly, annotating genomes, and conducting comparative analyses to uncover the evolutionary dynamics and functional diversity of bacterial species.

Aim: The aim of the Advanced Workshop on Bacterial Comparative Genomics is to equip participants with advanced knowledge and practical skills essential for analyzing bacterial genomes through comparative genomics methodologies. By the conclusion of the workshop, participants will possess the expertise needed to conduct sophisticated genomic analyses and contribute to advancements in bacterial genomics research.

Workshop Objectives:

  • Provide participants with the technical proficiency required to process and analyze read data for bacterial genomes.
  • Enable participants to perform de novo assembly, genome annotation, and comparative genomic analyses using state-of-the-art bioinformatics tools.
  • Foster an understanding of bacterial genome evolution, genetic diversity, and functional genomics.
  • Familiarize participants with tools for identifying antimicrobial resistance genes and conducting pangenome analyses to elucidate bacterial genome dynamics.
  • Introduce participants to Comparative Genomics Webservers for further exploration and analysis of bacterial genomes.
  • What you will learn?

    Day 1

    • Installing genomics tools with Conda
    • Obtaining reads Data
    • Perform QC and Trimming of Data
    • Perform de novo assembly using spades

    Day 2

    • Polish the draft assembly using pilon
    • Reordering contigs against a reference genome using ragtag
    • Multi-locus sequence typing
    • Annotate the draft genome using prokka

    Day 3

    • Look for antimicrobial resistance genes using abricate
    • Perform Pangenome Analysis
    • Overview of Comparative Genomics Webserver like BV-BRC

    Requirements:

    • Working knowledge of Linux OS system is a must for the workshop

    • PC with Linux operating system or Microsoft Windows Subsystem for Linux (see this link: https://www.freecodecamp.org/news/how-to-install-wsl2-windows-subsystem-for-linux-2-on-windows-10/)

    • Install conda. For installing conda in the Windows sub-system see the link: https://medium.com/@parham.motameni/install-conda-on-wsl2-2e76d1e03229

    Mentor Profile

    Dr. Subarna Thakur is an Assistant Professor in the Department of Bioinformatics at the University of North Bengal. She received his/her Ph.D. Degree in Botany from the University of North Bengal in 2014 and then worked as a Post Doc in various institutes like JNU, Bose Institute and IRHS, Angers, France for 4 Years. She is having more than 10 Years of Experience in the field of Computational Biology and Genomics. Her Area of Expertise includes NGS Data analysis, Transcriptomics, Network Biology. She is the author of 10 original research articles in high-impact peer-reviewed journals.

    Fee Plan

    Student

    INR 1399/- OR USD 50

    Ph.D. Scholar / Researcher

    INR 1699/- OR USD 55

    Academician / Faculty

    INR 2199/- OR USD 60

    Industry Professional

    INR 2699/- OR USD 85

    Important Dates and Time

    Registration Ends

    29 Mar 2024

    Indian Standard Timing 02:30 PM

    Workshop Dates

    29 Mar 2024 to 31 Mar 2024

    Indian Standard Timing 03:30 PM

    Get an e-Certificate of Participation!

    Intended for: Graduates, Post Graduates, Research Scholars, Academicians, Industry Professionals In the field of molecular biology, microbiology, bioinformatics, or related fields.

    Career Supporting Skills

    Genomic Data Analysis

    Bioinformatics Tools

    Pangenome Analysis

    Linux OS Proficiency

    Comparative Genomics Expertise

    Antimicrobial Resistance Identification

    Workshop Outcomes

  • Proficiency in Genomic Data AnalysisParticipants will master techniques for processing, analyzing, and interpreting genomic data, including read data QC, de novo assembly, and annotation, enabling them to conduct sophisticated genomic analyses.
  • Mastery of Bioinformatics Tools: Participants will gain hands-on experience with essential bioinformatics tools such as SPAdes, Pilon, RagTag, Prokka, and Abricate, equipping them with practical skills for genomic data analysis in research and industry settings.
  • Understanding of Comparative Genomics Principles: Participants will develop a deep understanding of comparative genomics principles and methodologies, enabling them to investigate bacterial genome evolution, genetic diversity, and functional genomics.
  • Identification of Antimicrobial Resistance Genes: Participants will acquire the expertise to identify antimicrobial resistance genes and interpret their significance in the context of public health, clinical microbiology, and antibiotic drug development.
  • Pangenome Analysis Skills: Participants will learn pangenome analysis techniques to explore bacterial genome dynamics, population genomics, and evolutionary biology research, providing valuable insights into microbial ecology and adaptation.
  • Effective Communication of Genomic Findings: Participants will enhance their communication skills to effectively present genomic findings and insights, facilitating scientific discourse, writing research papers, and collaborating with interdisciplinary teams.
  • Problem-Solving Abilities in Bioinformatics: Participants will develop problem-solving skills to address complex challenges in genomic data analysis, enabling them to overcome technical hurdles and advance genomic research agendas.
  • Linux OS Proficiency: Participants will gain strong foundational knowledge in Linux OS for bioinformatics analysis, empowering them to navigate command-line interfaces and perform computational analyses efficiently, essential for academic research and industrial applications.
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