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Article

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

by H. Richard Johnston; Pankaj Chopra; Thomas Wingo; Viren Patel; Michael Epstein; Jennifer Mulle; Stephen Warren; Michael Zwick; David Cutler

2017

Subjects
  • Biology, Genetics
  • Chemistry, Biochemistry
  • Biology, General
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Abstract:Close

The analysis of human whole-genome sequencing data presents significant computational challenges. The sheer size of datasets places an enormous burden on computational, disk array, and network resources. Here, we present an integrated computational package, PEMapper/PECaller, that was designed specifically to minimize the burden on networks and disk arrays, create output files that are minimal in size, and run in a highly computationally efficient way, with the single goal of enabling whole-genome sequencing at scale. In addition to improved computational efficiency, we implement a statistical framework that allows for a base by base error model, allowing this package to perform as well or better than the widely used Genome Analysis Toolkit (GATK) in all key measures of performance on human whole-genome sequences.
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