title: Training alignment parameters for arbitrary sequencers with LAST-TRAIN.
abstract: LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads.
  
  
  
  the source code is freely available at http://last.cbrc.jp/.
  
  
  
  mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.|Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.|Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.
authors.forename: Michiaki
authors.initials: M
authors.lastname: Hamada
authors.affiliation: IMSBIO Co, Ltd, Tokyo 170-0013, Japan.
authors.forename: Yukiteru
authors.initials: Y
authors.lastname: Ono
authors.affiliation: Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.|Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan.
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
authors.affiliation: Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.|Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.|Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan.
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
mesh_terms: D015894:Genome, Human; D006801:Humans; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software