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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.
RNA-seq has rapidly become the de facto technique to measure gene expression. However, the time required for analysis has not kept up with the pace of data generation. Here we introduce Sailfish, a novel computational method for quantifying the abund
We investigate usage of dynamic time warping (DTW) algorithm for aligning raw signal data from MinION sequencer. DTW is mostly using for fast alignment for selective sequencing to quickly determine whether a read comes from sequence of interest. We
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing (ESS) overcome
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we show that th
The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can