Cassavabase workshop in San Diego Jan 2014

Cassavabase and field book demo slides and exercises:

solGS: Estimating breeding values

April 2013 Training Courses in Nigeria

Umdike, April 2013

Ibadan, April 2013

Link to Slides from presentations

Online bioinformatics resources and tutorials

Topics that will be covered (details below)

Each session consists of ~1.5h of lectures, and ~2h of exercices.

Day 1

Session 1: Introduction to Genomics (probably no exercises for this session)
i)Basic Biology and Sequencing Technologies (Lukas)
ii)Applications: Genome Sequencing, RNASeq, GBS (Simon)

Session 2: CassavaBase 1 (Lukas)

Day 2

Session 3: Phytozome and Gbrowse (Simon)
Session 4: CassavaBase 2 (including time for discussion and questions) (Lukas)

Day 3

Session 5: Site specific requests: what other topics do scientists at Ibadan/Umudike want training on?
i) Sequence databases and sequence searching with BLAST alignment tools (+practical exercises)
ii) Multiple sequence alignments with muscle (+ practical exercises)

Detailed program

Day 1
Session1. Introduction to Genomics (Lukas & Simon)

  • Basic biology and sequencing technologies (Lukas)
  • DNA, RNA, Proteins
  • Sequencing LUKAS: here, please also discuss WGS sequencing compared to mRNA/EST/RNA-Seq sequencing
  • Sanger Sequencing
  • "Next-gen" sequencing
  • 454
  • Illumina
  • Restriction enzymes, polymerases for sequencing technology, PCR
  • Examples and problems

  • Applications: RNASeq and GBS (Simon)
  • Making RNA-Seq libraries
  • Making GBS libraries
  • Quality filtering Next-gen sequence data
  • Applications for RNA-Seq data: reconstructing transcripts and finding differentially-expressed genes.
  • Applications for GBS: genetic map making, Genomic Selection (covered in more detail by Jean-Luc who is visiting in May)
  • Examples and problems

Session 2. Cassavabase 1 (Lukas)

  • Introduction to the website
  • Searching
  • Genetic maps
  • The phenotype database
  • Ontologies - the cassava ontology, ontology viewer
  • curating phenotypes using the web interface
  • using the barcode reader for phenotyping
  • Examples and problems

Day 2
Session 3.
Phytozome and Gbrowse (Simon)
  • Overview of Phytozome
  • searching for data by keyword
  • searching by sequence similarity
  • Viewing data on the gene families
  • Viewing data on genes
  • Gbrowse genome viewer
  • Searching gbrowse by keyword
  • Retrieving large datasets from phytozome using the biomart interface.
  • Multiple sequence analysis with JalView

Session 4. Cassavabase 2 (Lukas)

  • Using the Breeder Home functions
  • Entering locations and trial information
  • Entering crosses

  • Barcodes
  • generating barcodes
  • Examples and problem set

Day 3
Session 5. Sequence similarity searches (Simon)
  • Common public sequence databases: swissprot, NCBI nr
  • Searching for similar sequences with blast

Session 6. Multiple sequence alignment with muscle (Lukas)
  • Using the muscle tool in Cassavabase.