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PEMapper and PECaller provide a simplified approach to whole-genome sequencing

Johnston, H. Richard, Chopra, Pankaj, Wingo, Thomas S., Patel, Viren, Epstein, Michael P., Mulle, Jennifer G., Warren, Stephen T., Zwick, Michael E., Cutler, David J. and Van Den Bree, Marianne 2017. PEMapper and PECaller provide a simplified approach to whole-genome sequencing. Proceedings of the National Academy of Sciences of the United States of America 114 (10) , E1923-E1932. 10.1073/pnas.1618065114

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Abstract

PEMapper and PECaller are paired software programs that simplify mapping and variant calling for whole-genome datasets. Whole-genome sequencing data are fast becoming the most natural dataset for all genetic studies. Analysis tools for data at this scale are essential. This manuscript describes tools, which solve the challenges of data analysis at whole-genome scale, using an approach involving 16-mer mapping and SNP calling based on a Pólya–Eggenberger distribution for SNP genotypes. We show that our software package is faster (cheaper to run), uses much less disk space (cheaper to store results), requires no previous knowledge of existing genetic variation (easier to deploy to nonhuman species), and achieves calling results that are as good as Genome Analysis Toolkit best practices.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
MRC Centre for Neuropsychiatric Genetics and Genomics (CNGG)
Publisher: National Academy of Sciences
ISSN: 0027-8424
Last Modified: 02 May 2019 15:04
URI: http://orca.cf.ac.uk/id/eprint/106960

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