The new sequencer on the block: comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing.

ABSTRACT: We assessed the performance of the new Life Technologies Proton sequencer by comparing whole-exome sequence data in a Centre d'Etude du Polymorphisme Humain trio (family 1463) to the Illumina HiSeq instrument. To simulate a typical user's results, we utilized the standard capture, alignment and variant calling methods specific to each platform. We restricted data analysis to include the capture region common to both methods. The Proton produced high quality data at a comparable average depth and read length, and the Ion Reporter variant caller identified 96 % of single nucleotide polymorphisms (SNPs) detected by the HiSeq and GATK pipeline. However, only 40 % of small insertion and deletion variants (indels) were identified by both methods. Usage of the trio structure and segregation of pl

SUBMITTER: Boland JF 

PROVIDER: S-EPMC4564298 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature