Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone

Bioinformatics

Volumn 30, Issue 24, 2014, Pages 3484-3490

  Trappe, Kathrin ^a,b   Emde, Anne Katrin ^c   Ehrlich, Hans Christian ^a   Reinert, Knut ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b ROBERT KOCH INSTITUTE   (Germany)

^c NEW YORK GENOME CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM; DNA SEQUENCE; GENE DELETION; GENE TRANSLOCATION; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; SEQUENCE ALIGNMENT;

GENOMIC STRUCTURAL VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SOFTWARE; TRANSLOCATION, GENETIC;

EID: 84922725524     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu431     Document Type: Article

References (26)

1. Abyzov, A. and Gerstein, M. (2011) AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics, 27, 595-603.
2. Abyzov, A. et al. (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res., 21, 974-984.
3. Alkan, C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363-376.
4. Brudno, M. et al. (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics, 19(Suppl 1), i54-i62.
5. Chen, K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-684.
6. Chen, K. et al. (2013) TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res, 24, 310-317.
7. Döring, A. et al. (2008) SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9, 11.
8. Emde, A.-K. et al. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28, 619-627.
9. Holtgrewe, M. (2010) Mason a read simulator for second generation sequencing data. In: Technical Report TR-B-10-06. Institut für Mathematik und Informatik, Freie Universität Berlin.
10. Hormozdiari, F. et al. (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19, 1270-1278.
11. Kececioglu, J. (1993) The maximum weight trace problem in multiple sequence alignment. In: Proceedings of the 4th Symposium on Combinatorial Pattern Matching (CPM) Padova, Italy. volume 684 of Lecture Notes in Computer Science. Springer-Verlag, pp. 106-119.
12. Kehr, B. Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12(Suppl 9), S15.
13. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
14. Maher, C. A. et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature, 458, 91-101.
15. Marschall, T. et al. (2012) CLEVER: clique-enumerating variant finder. Bioinformatics, 28, 2875-2882.
16. Marschall, T. et al. (2013) MATE-CLEVER: mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics, 29, 3143-3150.
17. Onishi-Seebacher, M. and Korbel, J. O. (2011) Challenges in studying genomic structural variant formation mechanisms: the short-read dilemma and beyond. Bioessays, 33, 840-850.
18. Paten, B. et al. (2008) Enredo and Pecan: genome-wide mammalian consistencybased multiple alignment with paralogs. Genome Res., 18, 1814-1828.
19. Pevzner, P. A. et al. (2004) De novo repeat classification and fragment assembly. Genome Res., 14, 1786-1796.
20. Rasmussen, K. R. et al. (2006) Efficient q-gram filters for finding all epsilon-matches over a given length. J. Comput. Biol., 13, 296-308.
21. Rausch, T. et al. (2012) DELLY: structural variant discovery by integrated pairedend and split-read analysis. Bioinformatics, 28, i333-i339.
22. Trappe, K. (2012) Multi-Split-Mapping of NGS reads for variant detection. Master's thesis, Department of Computer Science, Freie Universität Berlin, Berlin, Germany.
23. Tuzun, E. et al. (2005) Fine-scale structural variation of the human genome. Nat. Genet., 37, 727-732.
24. Xi, R. et al. (2011) Copy number variation detection in whole-genome sequencing data using the bayesian information criterion. Proc. Natl Acad. Sci. USA, 108, E1128-E1136.
25. Ye, K. et al. (2009) Pindel: pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.
26. Yoon, S. et al. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-1592.