Quality score compression improves genotyping accuracy
Name
Berger_Quality score.pdf
Size
671.39 KB
Format
Adobe PDF
Checksum (MD5)
973caf75876634a9da274de391f8e5fb
Author(s)
Yu, Yun William
Yorukoglu, Deniz
Peng, Jian
Berger Leighton, Bonnie
Date Issued
March 2015
Journal
Nature Biotechnology
Publisher
Springer Nature
Citation
Yu, Y William, Deniz Yorukoglu, Jian Peng, and Bonnie Berger. “Quality Score Compression Improves Genotyping Accuracy.” Nature Biotechnology 33, no. 3 (March 6, 2015): 240–243.
Version
Author's final manuscript
Abstract
To the Editor:
Most next-generation sequencing (NGS) quality scores are space intensive, redundant and often misleading. In this Correspondence, we recover quality information directly from sequence data using a compression tool named Quartz, rendering such scores redundant and yielding substantially better space and time efficiencies for storage and analysis. Quartz is designed to operate on NGS reads in FASTQ format, but it can be trivially modified to discard quality scores in other formats for which scores are paired with sequence information. Discarding 95% of quality scores resulted, counterintuitively, in improved SNP calling, implying that compression need not come at the expense of accuracy.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Mathematics
Terms of Use
Creative Commons Attribution-Noncommercial-Share Alike
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1038/nbt.3170
