Bioinformatics 101 – 2019: Introduction to methods and tools for NGS analysis

Offered by the ICBR Bioinformatics core, in collaboration with the UFHCC BQS SR and HSC Library.

Overview

This course consists of eight lectures covering Next-Gen Sequencing data generation and computational analysis. Hands-on exercises will be performed on HiPerGator.

Registration Policy: there is no registration fee but please register by January 18. You may attend selected lectures at your discretion.

This course is not for credit, but those who complete the course will receive a certificate.

 

Instructors

  • Alberto Riva, ICBR Bioinformatics Core and UFHCC BQS SR (coordinator)
  • Brad Barbazuk, ICBR Bioinformatics Core and UFHCC BQS SR
  • Lucas Boatwhight, ICBR Bioinformatics Core
  • Ana Conesa, Dept of Microbiology and Cell Science and UFHCC BQS SR

 

Syllabus

The course will take place in the HSC Library Computer Lab, room C1-121 (Communicore), 4-5pm. All lectures are scheduled for Tuesdays, except for the last one which takes place on a Thursday.

Date Topic Videos Slides Instructors
1/22/2019 Introduction to Next-Gen Sequencing – High-throughput sequencing technologies, sample preparation, sequencing strategies. video BB
1/29/2019 Introduction to command-line – Basic shell commands, file system operations, text file manipulation, simple scripting. video slides AR, LB
2/5/2019 HiPerGator usage – Job creation and submission, job control, parallelization, pipelines. video slides AR, LB
2/12/2019 Basic Next-Gen analysis – Quality control, read trimming and filtering, read alignment. video slides AR, LB
2/19/2016 Advanced Next-Gen analysis – RNA-Seq, ChIP-Seq. video slides AR, LB
2/26/2019 Advanced Next-Gen analysis – Methylation analysis, Variant calling. video slides AR, LB
3/12/2019 Advanced applications – Functional annotation of sequence data. video slides AC
3/14/2019 Advanced applications – Functional profiling of omics experiments. video slides AC

 

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