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WORKSHOP: Basic bioinformatics and command-line tools for phytopathologists: How to handle, explore, and organize big biological data.​

​Broadcast Date: Tuesday, October 26, 2021 | 11:00 AM –​ 4:00 PM US Central Time​​

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High-throughput sequencing technologies have significantly improved the generation of large data sets of omics information (genomes, transcriptomes, proteomics and microbiomes). Administration and analysis of big data in the omics-era to understand complex biological systems present a new challenge for plant pathologists. Analysis of big and complex data sets requires use of computational tools that interact with databases and computer servers. The command line interface allows users to interact with computers both locally and in server to conduct computationally intensive analyses. In this workshop, we will explore different usages of command line interface for bioinformatic analyses. We will introduce the cluster computing system, Linux shell, and shell scripting. We will use unix commands to parse sequence and text files followed by application of local BLAST and data parsing.

Learning Objectives

  • The participants will learn command line tools for bioinformatics analyses and use of cluster computing that commonly used in microbial genomics studies.

Target Audience

Plant pathologists interested to apply computational tools for analyzing high-throughput sequencing data using cluster computers. Participants are expected to have some idea about genomic data, sequencing platforms, and general terminologies commonly used in bioinformatics such as assembly, annotation, sequencing platforms, fastq, fasta, etc. No technical proficiency is expected. Participants should bring their computers (Windows, Mac, or Unix). Windows user are requested to bring computers with administrative access. The workshop will provide contents from​


Sujan Timilsina, University of Florida
Jose C. Huguet-Tapia, University of Florida
Erica M. Goss, University of Florida 


Anuj Sharma, University of Florida
Liliana M. Cano, University of Florida