Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

Bioinformatics

Volumn 25, Issue 21, 2009, Pages 2865-2871

  Ye, Kai ^a,b   Schulz, Marcel H ^a,c   Long, Quan ^d   Apweiler, Rolf ^a   Ning, Zemin ^d  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^c MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; COMPUTER MEMORY; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE DELETION; GENE INSERTION; GENE MAPPING; GENETIC DIFFERENCE; GENOME ANALYSIS; HUMAN GENOME; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CHROMOSOME BREAKPOINTS; COMPUTATIONAL BIOLOGY; DNA BREAKS; GENOME; INDEL MUTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 70350694443     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp394     Document Type: Article

References (14)

1. Bennett,E.A. et al. (2004) Natural genetic variation caused by transposable elements in humans. Genetics, 168, 933-951.
2. Bentley,D.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
3. Chaisson,M.J. and Pevzner,P.A. (2008) Short read fragment assembly of bacterial genomes. Genome Res., 18, 324-330.
4. Iafrate,A.J. et al. (2004) Detection of large-scale variation in the human genome. Nat. Genet., 36, 949-951.
5. Kidd,J.M. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.
6. Levy,S. et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5, e254.
7. Mills,R.E. et al. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res., 16, 1182-1190.
8. Ning,Z. et al. (2001) SSAHA: A fast search method for large DNA databases. Genome Res., 11, 1725-1729.
9. Pei,J. et al. (2004) Mining sequential patterns by pattern-growth: The prefixspan approach. IEEE Trans. Knowl. Data Eng., 16, 1424-1440.
10. Schulz,M.H. et al. (2008) The generalised k-truncated suffix tree for time-and space-efficient searches in multiple DNA or protein sequences. Int. J. Bioinform. Res. Appl., 4, 81-95.
11. Sebat,J. et al. (2004) Large-scale copy number polymorphism in the human genome. Science, 305, 525-528.
12. Smit,A.F.A. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
13. Ye,K. et al. (2007) An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences. Bioinformatics, 23, 687-693.
14. Zerbino,D.R. and Birney,E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.