  In the last decade a number of algorithms and associated software have been
developed to align next generation sequencing (NGS) reads with relevant
reference genomes. The accuracy of these programs may vary significantly,
especially when the NGS reads are quite different from the available reference
genome. We propose a benchmark to assess accuracy of short reads mapping based
on the pre-computed global alignment of related genome sequences.
  In this paper we propose a benchmark to assess accuracy of the short reads
mapping based on the pre-computed global alignment of closely related genome
sequences. We outline the method and also present a short report of an
experiment performed on five popular alignment tools based on the pairwise
alignments of Escherichia coli O6 CFT073 genome with genomes of seven other
bacteria.
