I am working in the Schatz Lab during the summer of 2012 as part of Cold Spring
Harbor Laboratory's Undergraduate Research
Program. My work is focusing on de novo genome assembly of highly
heterozygous genomes. Current assemblers for short reads from the Illumina
platform, such as the Allpaths-LG
assembler, produce very poor assemblies if the genomes contains a high level
of heterozygosity. In order to aid the assembly process, we are developing a
technique for preprocessing the reads to reduce the amount of heterozygosity.
After an initial assembly is created, the original reads could then mapped onto
the assembled genome to recover the heterozygosity.
We initially plan to use this technique on the genome for Ananas comosus, the
pineapple plant. The pineapple plant has a high rate of heterozygosity;
possibly 1 in 50 base pairs differ between homologous chromosomes, compared to
about 1 in 1000 for the human genome. As a result, the Allpaths-LG assembler
has been unable to adequately assemble the pineapple genome from short Illumina
reads. We aim to produce a usable draft assembly of the pineapple genome to
demonstrate our technique for assembling heterozygous genomes.
I am currently a student at Macalester College in St. Paul, Minnesota, where I
am double majoring in Computer Science and Mathematics.
Eric Biggers |
Cold Spring Harbor Laboratory
One Bungtown Road
Koch Building 1124
Cold Spring Harbor, NY 11724
E-mail: ebiggers <at> cshl.edu