The single nucleotide polymorphism (SNP) is the most widely studied type of
genetic variation. A haplotype is defined as the sequence of alleles at SNP
sites on each haploid chromosome. Haplotype information is essential in
unravelling the genome-phenotype association. Haplotype assembly is a
well-known approach for reconstructing haplotypes, exploiting reads generated
by DNA sequencing devices. The Minimum Error Correction (MEC) metric is often
used for reconstruction of haplotypes from reads. However, problems with the
MEC metric have been reported. Here, we investigate the MEC approach to
demonstrate that it may result in incorrectly reconstructed haplotypes for
devices that produce error-prone long reads. Specifically, we evaluate this
approach for devices developed by Illumina, Pacific BioSciences and Oxford
Nanopore Technologies. We show that imprecise haplotypes may be reconstructed
with a lower MEC than that of the exact haplotype. The performance of MEC is
explored for different coverage levels and error rates of data. Our simulation
results reveal that in order to avoid incorrect MEC-based haplotypes, a
coverage of 25 is needed for reads generated by Pacific BioSciences RS systems.Comment: 17 pages, 6 figure