Workshop on Apicomplexan Genome Analysis

Workshop on Apicomplexan Genome Analysis

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In September 2016, Dr. Hernan Lorenzi (JCVI) and collaborators Chunlei Su and Solange Gennary and organized a 5-day workshop on Apicomplexan Genome Analysis in the Department of Preventive Veterinary Medicine at the University of São Paulo, Brazil. Participants in the workshop included 20 scientists, postdoctoral fellows and PhD students from South and Central America. 

The main goal of this hands-on workshop was to let participant scientists learn the cutting-edge technology in whole genome sequence analysis and utilization of sequencing data produced as part of the GCID Parasites project at JCVI to study population genetics and functional genomics of apicomplexan parasites.

The workshop consisted of two morning lectures each day followed by afternoon hands-on bioinformatics practices in a computer lab, where participants learned how to:

  1. retrieve and manipulate different kinds of omics sequencing data (sequencing reads, SNPs, genome assemblies, RNAseq reads, annotation data, etc.) from public repositories, including EuPathDB and GenBank;
  2. map sequencing reads to reference genomes for SNP identification;
  3. annotate SNPs (finding SNPs and InDels that cause frame-shifts, missense mutations, etc.);
  4. build SNP-based phylogenetic networks for studying parasite population structure and 5) generate RNAseq-based gene expression data and perform differential gene expression analyses. A detailed summary of the topics that were discussed each day can be found here (link to workshop syllabus).

During the last day, participanting scientists and students gave an informal 15 min. talk describing their research projects and how they would benefit from what they had learnt in the workshop, where they received feedback from all instructors.

Each participant had access to a desktop computer running a virtual Linux machine with all the required software ready to run, including a step-by-step pipeline for mapping new sequencing reads to a reference genome followed by SNP discovery, annotation and analysis of population structure. By the end of the workshop, a ready-to-use virtual machine was made available to participants through an FTP site at the University of Sao Paulo, so it could be downloaded at the participants’ institutions for running all the analyses learnt during the course on their own datasets.

The workshop was supported in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Numbers R13AI126819 and U19AI110819 and the University of São Paulo, Brazil.