The “Programa de Pós-Graduação em Fitopatologia”, as part of the dual degree agreement with the Department of Plant Pathology of the University of Kentucky, will be hosting a workshop covering the acquisition and bioinformatic analysis of Next Generation Sequencing (NGS) data.

Workshop goals

To provide participants with an understanding of the technical aspects of data acquisition, and an introduction to the use of common (and open source) tools for data analysis (genomic, RNAseq and metagenomic data sets). No prior experience or background in NGS is required.

Basic requirements

• Basic skills in English (conversation and understanding). The workshop will be in English.
• Applicant’s research/knowledge in bioinformatics, but beyond editing and alignment of sequences and phylogenetic analysis (see activities below).
• Familiarity with command-line interfaces (Unix, Linux).
• Notebook computer with at least 4Gb RAM, desirable 8Gb.

Who are encouraged to apply?

• Graduate students,  postdocs and faculty members of the University
• Preference will be given to (as long as the requirements are met):
  • Graduate students members of GEAFIP
  • PNPD postdoc researchers of the PPG Fitopatologia

Organizers

Prof. Mark Farman, Dept of Plant Pathology, University of Kentucky
Prof. Eduardo Mizubuti, Depto de Fitopatologia, Universidade Federal de Viçosa

How to apply?

Send an email to mizubuti@ufv.br introducing yourself and justifying your application. Deadline:  October 23rd

Workshop details

Workshop Fee: R$200,00.
Load: Approximately 30 hours.

Schedule:

Bioinformatics activities

• Linux essentials
• File formats and quality assessment:  FastQC, Trimmomatic
• Sequence assembly: Velvet, Discovar de novo
• Sequence search and alignment: Blast, Samtools, Tophat2
• Transcript assembly and quantification: Cufflinks, Cuffmerge, Cuffdiff
• Variant detection: Samtools mpileup
• Gene finding: Augustus, SNAP and MAKER
• Data visualization:  Integrated Genome Viewer
• Metagenomics: QIIME