April 10, 2013

Topic: Population scale sequencing
Discussion Leader: Louis
Paper: Lamichhaney et al. 2013

Supplementary information

Nov. 5, 2012

Topic: Transcriptome assembly

Discussion leader:  Yash

Papers:  Martin and Wang 2011
             Sun et al. 2012

Discussion questions

Oct. 1, 2012

Topic: Genome assembly

Discussion leader:  Sandy

Readings: Haridas et al. 2011 + Supplementary data
                 Pop et al. 2009

Hands-on activity: Assembling 454 reads

1. Sign up for an account at iPlant
2. Login to the Discovery Environment
3. Navigate Apps>Public Applications>NGS>Assemblers
4. Open Newbler 2.6.0
5. Click the add button to add a .sff file of 454 reads
6. The file is under Community Data>iplantcollaborative>example_data>Newbler-2.6.0 and it is called FFGLB5S034.sff
7. Select "under 1h" for the run time under Run Options. Leave other defaults in place, launch and name the job.
8. You'll receive an email when the job has completed.
9. Go to your data folder under "analyses."
10. The assembled contigs will be under NewblerOutput>454AllContigs.fna.
11. Open this file to see the assembled genes. Some of the contigs have lower-case base letter - what do you think that means?
12. Paste a few of them into NCBI blast -- what species are they from?