Training alignment parameters for arbitrary sequencers with LAST-TRAIN

Bioinformatics

Volumn 33, Issue 6, 2017, Pages 926-928

  Hamada, Michiaki ^a,b   Ono, Yukiteru ^c   Asai, Kiyoshi ^b,d   Frith, Martin C ^b,d   Hancock, John ^e  

^a WASEDA UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c IMSBIO Co   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

^e NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCE; GENETIC POLYMORPHISM; HUMAN; HUMAN GENOME; PROCEDURES; SOFTWARE;

GENOME, HUMAN; HUMANS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85018244647     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw742     Document Type: Article

References (15)

1. Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Ammar, R. et al. (2015) Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000Res, 4, 17.
3. Chaisson, M.J. and Tesler, G. (2012) Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics, 13, 238.
4. Chiaromonte, F. et al. (2002) Scoring pairwise genomic sequence alignments. Pac. Symp. Biocomput., 115-126. pages
5. Durbin, R. et al. (1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
6. Frith, M., and Kawaguchi, R. (2015) Split-alignment of genomes finds orthologies more accurately. Genome Biol., 16, 106-106.
7. Hamada, M. et al. (2011) Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinformatics, 27, 3085-3092.
8. Jain, M. et al. (2015) Improved data analysis for the MinION nanopore sequencer. Nat. Methods, 12, 351-356.
9. Kerpedjiev, P. et al. (2014) Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC Bioinformatics, 15, 100.
10. Laver, T.W. et al. (2016) Pitfalls of haplotype phasing from amplicon-based long-read sequencing. Sci. Rep., 6, 21746.
11. Numanagi, I. et al. (2015) Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data. Bioinformatics, 31, 27-34.
12. Sovic, I. et al. (2016) Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat. Commun., 7, 11307.
13. States, D.J. et al. (1991) Improved sensitivity of nucleic acid database similarity searches using application specific scoring matrices. Methods, 3, 66-70.
14. Twist, G.P. et al. (2016) Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences. Npj Genomic Med., 1, 15007.
15. Zhang, Z. et al. (1998) Alignments without low-scoring regions. J. Comput. Biol., 5, 197-210.