FastUniq: a Fast De Novo Duplicates Removal Tool for Paired Short Reads

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2013 Jan 4

PMID 23284954

Citations 282

Authors

Haibin Xu

Xiang Luo

Jun Qian

Xiaohui Pang

Jingyuan Song

Guangrui Qian

Jinhui Chen

Shilin Chen

Affiliations

Soon will be listed here.

Abstract

The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time, which increases linearly at an average speed of 87 million reads per 10 minutes. FastUniq is freely available at http://sourceforge.net/projects/fastuniq/.

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