This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. At the beginning of 2010 I started a faculty position in bioinformatics at the University of Nebraska Medical Center (UNMC). My responsibilities include support for bioinformatics and genomics related to the analysis of next-generations (DNA) sequencing data, or NGS data. UNMC has very limited hardware and software infrastructure for research computing. Several UNMC investigators (most of whom are NIH funded) need to perform large-scale mammalian genome assembly tasks that are well beyond our compute capabilities, and require the use of genome assembly software that is challenging to deploy and support. The Pople resource at the PSC provide the ABySS genome assembly software that is ideal for our large-scale genome assembly needs, and hence in the first instance we seek to use that software and resource. The first project involves the de novo assembly of 90-100 Gigabases of Illumina 2x75bp paired-end DNA sequencing reads from the genome of the same rhesus monkey whose genome was sequenced by investigators at the Baylor College of Medicine. In this first project our goal is to improve the existing 5x coverage-depth draft rhesus genome assembly described in the paper Evolutionary and biomedical insights from the rhesus macaque genome (www.ncbi.nlm.nih.gov/pubmed/17431167) via merging of this existing draft assembly with an ABySS-generated de novo assembly obtained from 30x coverage-depth Illumina NGS read data generated by a UNMC faculty colleague.
Showing the most recent 10 out of 292 publications
