Eric Biggers

Research Interests

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.

Other Information

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>