Project Summary
The horse genome (equus caballus) was recently sequenced by
Broad Institute
using the
Arachne Assembler.
My goal is to resequence the genome
using the Celera Assembler
and then produce a consensus sequence that is more
accurate than either of the original assemblies. This project is intended to
satisfy the course requirements of AMSC 663 and AMSC 664.
Advisor
My advisor is Jim Yorke. I will be
working extensively with his genome group throughout the duration of this project.
Project Proposal
Power Point Presentation
Written Proposal
Midyear Report
Power Point Presentation
Written Report
Spring Report
Power Point Presentation
Final Report
Power Point Presentation
Written Report
News
(4/25/08) Successfully ran my prallelized overlapper on the horse (took 3 days and 1 hour)
(4/14/08) Obtained results from reconciliation (Stats)
(3/31/08) Successfully ran my parallelized overlapper on the fly
(3/30/08) Ran reconciliation software on my assembly of the horse and
Broad's assembly
(3/5/08) Compared Celera supercontigs to Arachne supercontigs (2078/2252 matched)
(3/2/08) Created parallelized version of overlapper that runs successfully on bacteria
(12/21/07) Finished running the Celera Assembler (Stats)
(12/12/07) Started running the Celera Assembler
(11/23/07) Finished running the overlapper
(10/16/07) Modified the .frg file to reflect the trim values
(10/13/07) Generated a .frg file
(10/13/07) Ran vector trimmer on all of the reads
(9/30/07) Created new fasta files sorted by library