A solid quality-control analysis of AB SOLiD short-read sequencing data

被引：6

作者：

Castellana, Stefano

Romani, Marta

Valente, Enza Maria

Mazza, Tommaso

机构：

[1] The Bioinformatics Unit, CSS-Mendel Institute

[2] Neurogenetics Unit, CSS-Mendel Institute

来源：

BRIEFINGS IN BIOINFORMATICS | 2013年 / 14卷 / 06期

关键词：

genetics; next generation sequencing; sequencing quality control; GENERATION; ERROR;

D O I：

10.1093/bib/bbs048

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

Next generation sequencers have greatly improved our ability to mine polymorphisms and mutations out of entire (or portions of) genomes. The reliability of their outputs, though, showed to be very related to the sequencing chemistry and to deeply affect the quality of the downstream analyses. We focus here on the two-base color code chemistry of AB SOLiD sequencers and propose a comprehensive quality control methodological and software pipeline. We used existing and custom tools to detect and purge short-reads of some common flaws due to sequencing errors and chemical hitches. We apply them to a cohort of SOLiD 4 runs and measure their joint efficacy in terms of the resulting ability to detect the greatest possible number of true variants.

引用

页码：684 / 695

页数：12

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