Pan African Bioinformatics Network for H3Africa

Next Generation Sequencing Workshops October 2014 - Presented by Dean Bobo, Stony Brook University

Join us for 2 weeks of workshops and Q&A sessions with Mr. Dean Bobo from the Henn Lab for Population Genetics, Stony Brook University, NY. Dean received his Bachelor’s degree from Ramapo College of New Jersey with a major in biology and minors in bioinformatics and chemistry. He completed a bioinformatics research internship at the Boyce Thompson Institute for Plant Research at Cornell University. There he worked on bioinformatics web tools and databases for the SOL Genomics Network, which was sequencing the tomato (Solanum lycopersicum). Dean then went on to Johns Hopkins University and obtained his Master’s in Biotechnology. In March of 2013, he joined the Henn Lab as a bioinformatics scientist and is studying human evolution and population genetics of the Out-of-Africa migration.

Date  Time  Topic 
Wed,1 October  9.30am-11.30am  Lecture- NGS technology (fastq files and SAM tools)
 1pm  Lab
Thurs, 2 October  9.30am-12.30pm  Q&A
Fri, 3 October 10.30am-12.30pm Lecture- BAM file manipulation
2pm Lab
Mon, 6 October 10.30am-12.30pm Lecture- GATK suite (QC and statistics)
2pm Lab
Tues, 7 October 9.30am-12.30pm Q&A
Wed, 8 October 9.30am-11.30am Lecture- calling variants (Haplotypecaller)
1pm  Lab
Thurs, 9 October 9.30am-12.30pm Q&A
Fri, 10 October 10.30am-12.30pm Lecture- VCF file manipulation
2pm  Lab


  • All lectures and labs will be held in the Department of Molecular Biology and Human Genetics Seminar Room,
  • 4th Floor Fisan Building, Stellenbosch University, Tygerberg Campus. Snacks will be provided.
  • It is suggested that all lectures and labs are attended, as they will follow on from one another.
  • Q&A sessions will be on a first come first serve basis.
  • Previous knowledge of the Unix shell, linux basic commands, R and python is required.
  • Please bring your own laptops to the approximately 2 hour long labs in the afternoon, no computers will be
  • available.
  • Please send a short motivation to This email address is being protected from spambots. You need JavaScript enabled to view it. by 15 September if you wish to attend, as space is
  • limited.

Please note that no accommodation or travel funding is available. Confirmation of attendance will be
sent by 19 September.