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Plant Health Workshop

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

On Demand Workshop

On Demand video is available ​to both workshop registrants and Unlimited Plant Health 2020 registrants.

Interested in learning more about this workshop topic outside of this event?
Check out Population Biology of Plant Pathogens: Genetics, Ecology, and Evolution and The Study of Plant Disease Epidemics from APS PRESS​.
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Workshop Description:​

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. Different genome data analyses using command line interface will be discussed.

Workshop Organizers

Sujan Timilsina, U​niversity of Florida, Gainesville, FL; Jose Huguet-Tapia, University of Florida, Gainesville, FL; Erica Goss, University of Florida, Gainesville, FL


Liliana Cano, University of Florida, UF/IFAS, IRREC, Plant Pathology, Fort Pierce, FL; Jose Huguet-Tapia, University of Florida, Gainesville, FL​; Anuj Sharma, University of Florida, Gainesville, FL