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. 2017 Mar 15;33(6):926-928.
doi: 10.1093/bioinformatics/btw742.

Training alignment parameters for arbitrary sequencers with LAST-TRAIN

Michiaki Hamada  1   2   3 , Yukiteru Ono  4 , Kiyoshi Asai  3   5 , Martin C Frith  2   3   5
Affiliations

Training alignment parameters for arbitrary sequencers with LAST-TRAIN

Michiaki Hamada et al. Bioinformatics. .

Abstract

Summary: 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.

Availability and implementation: the source code is freely available at http://last.cbrc.jp/.

Contact: mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp.

Supplementary information: Supplementary data are available at Bioinformatics online.

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