ReviSTER: An automated pipeline to revise misaligned reads to simple tandem repeats

Bioinformatics

Volumn 29, Issue 14, 2013, Pages 1734-1741

  Tae, Hongseok ^a   McMahon, Kevin W ^a   Settlage, Robert E ^a   Bavarva, Jasmin H ^a   Garner, Harold R ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; EXOME; GENOMICS; GENOTYPING TECHNIQUE; HAPLOIDY; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; SEQUENCE ALIGNMENT; TANDEM REPEAT; PROCEDURES;

ALLELES; EXOME; GENOMICS; GENOTYPING TECHNIQUES; HAPLOIDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; TANDEM REPEAT SEQUENCES;

EID: 84880247474     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt277     Document Type: Article

References (22)

1. Albers, C.A. et al. (2011) Dindel: accurate indel calls from short-read data. Genome Res., 21, 961-973.
2. Batzer, M.A. and Deininger, P.L. (2002) Alu repeats and human genomic diversity. Nat. Rev. Genet., 3, 370-379.
3. Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
4. Edwards, A. et al. (1991) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet., 49, 746-756.
5. Gymrek, M. et al. (2012) lobSTR: a short tandem repeat profiler for personal genomes. Genome Res., 22, 1154-1162.
6. HanCock, J.M. (1999) Microsatellites and other simple sequences: genomic context and mutational mechanisms. In: Goldstein, D.B. and Schlotterer, C. (eds) Microsatellites: Evolution and applications. Oxford University Press, New York, pp. 1-9.
7. Highnam, G. et al. (2012) Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles. Nucleic Acids Res., 41, e32.
8. Homer, N. and Nelson, S.F. (2010) Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol., 11, R99.
9. Hu, X. et al. (2012) pIRS: profile-based Illumina pair-end reads simulator. Bioinformatics, 28, 1533-1535.
10. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
11. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
12. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
13. Li, H. et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
14. Li, S. et al. (2013) SOAPindel: efficient identification of indels from short paired reads. Genome Res., 23, 195-200.
15. Mackay, T.F. et al. (2012) The Drosophila melanogaster Genetic Reference Panel. Nature, 482, 173-178.
16. McIver, L.J. et al. (2011) Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments. Genomics, 97, 193-199.
17. McKenna, A. et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
18. Scally, A. and Durbin, R. (2012) Revising the human mutation rate: implications for understanding human evolution. Nat. Rev. Genet., 13, 745-753.
19. Tae, H. et al. (2011) Revised genome sequence of Brucella suis 1330. J. Bacteriol., 193, 6410.
20. Tae, H. et al. (2012a) Complete genome sequence of Brucella suis VBI22, isolated from bovine milk. J. Bacteriol., 194, 910.
21. Tae, H. et al. (2012b) Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes. Genomics, 100, 271-276.
22. Ye, K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.