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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.
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Long et al. (2009) studied this question.
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