Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

@article{Hamada2011ProbabilisticAW,
  title={Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection},
  author={Michiaki Hamada and Edward Wijaya and M. Frith and K. Asai},
  journal={Bioinformatics},
  year={2011},
  volume={27 22},
  pages={
          3085-92
        }
}
MOTIVATION Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although… Expand
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