NextGenMap: Fast and accurate read mapping in highly polymorphic genomes

Bioinformatics

Volumn 29, Issue 21, 2013, Pages 2790-2791

  Sedlazeck, Fritz J ^a   Rescheneder, Philipp ^a   Von Haeseler, Arndt ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM; GENETIC POLYMORPHISM; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; SEQUENCE ALIGNMENT; ARTICLE; METHODOLOGY;

GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84885997727     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt468     Document Type: Article

References (10)

1. Dinh, H.Q. et al. (2012) Advanced methylome analysis after bisulfite deep sequencing: an example in arabidopsis. PLoS One, 7, e41528.
2. Fonseca, N.A. et al. (2012) Tools for mapping high-throughput sequencing data. Bioinformatics, 28, 3169-3177.
3. Holtgrewe, M. (2010) Mason a read simulator for second generation sequencing data. Technical Report TR-B-10-06, Institut für Mathematik und Informatik, Freie Universität Berlin, Available at http://edocs.fu-berlin. de/docs/receive/FUDOCS-document-000000006687 (28 August 2013, date last accessed).
4. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with bowtie 2. Nat. Methods, 9, 357-359.
5. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with BurrowsWheeler transform. Bioinformatics, 25, 1754-1760.
6. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with BurrowsWheeler transform. Bioinformatics, 26, 589-595.
7. Lunter, G. and Goodson, M. (2011) Stampy: a statistical algorithm for sensitive and fast mapping of illumina sequence reads. Genome Res., 21, 936-939.
8. Nielsen, R. et al. (2011) Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12, 443-451.
9. Rescheneder, P. et al. (2012) Mason: million alignments in seconds. In: Proceedings of the International Conference on Bioinformatics: Models, Methods and Algorithms. SciTePress, Setubal, Portugal, pp. 195-201.
10. Vesely, C. et al. (2012) Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res., 22, 1468-1476.