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Bioinformatics Advance Access published online on July 1, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp412
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

HI: Haplotype Improver using paired-end short reads

Quan Long *, Daniel MacArthur , Zemin Ning and Chris Tyler-Smith

The Wellcome Trust Sanger Institute, Hinxton, Cambs. CB10 1SA, UK.

*To whom correspondence should be addressed. Dr. Quan Long, E-mail: ql2{at}sanger.ac.uk


  Abstract

Summary: We present a program to improve haplotype reconstruction by incorporating information from paired-end reads, and demonstrate its utility on simulated data. We find that given a fixed coverage, longer reads (implying fewer of them) are preferable.

Availability: The executable and user manual can be freely downloaded from ftp://ftp.sanger.ac.uk/pub/zn1/HI.

Contact: ql2{at}sanger.ac.uk

Associate Editor: Prof. Alfonso Valencia

Received on April 27, 2009; revised on June 25, 2009; accepted on June 25, 2009

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