Oct 18th, 2022
11:00 am - 4:00 pm Eastern time
Instructors: Jose C. Huguet-Tapia, Braham Dhillon
Moderators: Liliana Cano, Erica M. Goss, Anuj Sharma
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 remote 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 Linux shell, cluster computing system, and shell scripting. We will use unix commands and command line programs to run BLAST locally, parse sequence and develop phylogenetic tree. Different genome data analyses using command line interface will be discussed.
Who: 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.
Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.
When: Oct 18th, 2022, 11:00 am - 4:00 pm Eastern time.
Requirements: Participants must bring a personal computer with Windows, MacOS or Linux operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages listed here installed on their computer. The organizers will share extensive pre- and post- meeting support materials including the codes, coding references, datasets, reading materials, and respective examples to the participants via workshop webpage and workshop github repository that can be accessed at any time during as well as after the conference.
Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.
Contact: Please email jhuguet@ufl.edu or dhillonb@ufl.edu for more information about the content. For technical problems regarding the website, email anujsharma@ufl.edu.
Please be sure to complete these surveys before and after the workshop.
| Time | Particulars |
|---|---|
| Before starting | Pre-workshop survey |
| 11:00 am - 11:05 am | Welcome remarks |
| 11:05 am - 11:15 am | Introduction (by Dr. Anuj Sharma) |
| Part 1 | Instructor: Dr. Jose C. Huguet-Tapia |
| 11:15 am - 12:30 pm | Basic tools and unix command line |
| 12:30 pm - 12:40 pm | Break |
| 12:40 pm - 12:55 pm | Running SLURM single thread script |
| 12:55 pm - 1:30 pm | Basic Local Alignment Search Tool (BLAST) |
| 1:30 pm - 1:45 pm | Break |
| Part 2 | Instructor: Dr. Braham Dhillon |
| 1:45 pm - 2:40 pm | Parsing BLAST output |
| 2:40 pm - 2:50 pm | Break |
| 2:50 pm - 3:30 pm | Running Phylogenetic tools |
| 3:30 pm - 3:45 pm | Follow up questions during workshop |
| 3:55 pm - 4:00 pm | Closing remarks (by Dr. Erica M. Goss) and Post-workshop survey |
Done with the regular course? Here are some more advanced lessons.
Go to this page for setup instructions.