2009-10-28 - Viruses and Drosophila

Status of the Sequencer - Donna Storton and Jessica Buckles

• Sequencer is running smoothly at high capacity
• Queue length is two runs (~2 weeks until newly submitted samples can be started)

HTSEQ Wiki and Public Website - Lance Parsons and John Matese

• The HTSEQ Wiki is a place where people can post comments, suggestions, and collect information about what strategies and tools have been useful
• We will create a listserv as well to facilitate communication to the members.

Virus strain sequencing, assembly, and variance detection - Moriah Szpara

• For a 160kb genome, one lane gives very high coverage (1000x)
• Multiplexing would be a very good option for this application - suggestions or tips anyone?
• Considering reducing the amount of data to improve contig creation (use only 10%?)
• Reiterations have been problematic, sometimes breaking contigs
  • Paired end may help with this somewhat, but likely PCR is required to get true sequence
• Contig assembly is extremely tedious - suggestions on approaches to this would be most welcome

Drosophila sequence assembly - Amy Caudy

• Investigation of herterochromatin regions of chromosome 2
• Align reads to the known reference and assemble the remaining reads to obtain contigs that may be from "interesting" regions
• Design probes for these contigs and use an array to profile various mutants
• Attempt to identify contigs that come from genes
• Contigs are quite small (~100 bp) - suggestions for helping to increase length?