I am working in the Schatz Lab during the summer of 2014 as part of Cold Spring
Harbor Laboratory's Undergraduate Research
Program. I am working on de novo genome assembly and whole genome alignment.
Currently, when assembling genomes from short Illumina reads, a reference genome is used
if one is available. However, aligning to a reference can only detect minor changes such as
SNPs or small indels. To detect larger structural variation between genomes, such as translocations,
inversions, or large insertions or deletions, de novo assembly must be used.
I will be streamlining the process of de novo assembly and whole genome alignment previously
performed by the Schatz Lab on
rice genomes. This will involve using the
Allpaths-LG assembler and the alignment program MUMmer, and doing
some additional analysis on the genomes, including looking at k-mer coverage across the genome. After streamlining
the process, it will be applied to other genomes in hopes of finding novel variations, including yeast genomes,
Solanaceae genomes, and human genomes of siblings/parents with and without autism, schizophrenia, and cancer.
I am currently a student at Harvey Mudd College in Claremont, CA. I am majoring in
Mathematical and Computational Biology, and will graduate in May 2015.
Rachel Sherman |
Cold Spring Harbor Laboratory
One Bungtown Road
Cold Spring Harbor, NY 11724