SEED: Efficient clustering of next-generation sequences

Bioinformatics

Volumn 27, Issue 18, 2011, Pages 2502-2509

  Bao, Ergude ^a   Jiang, Tao ^a   Kaloshian, Isgouhi ^b   Girke, Thomas ^b  

^a University of California Riverside   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTOME;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENOME; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

ALGORITHMS; BASE SEQUENCE; CLUSTER ANALYSIS; GENOME; MICRORNAS; SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTOME;

EID: 80052722558     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr447     Document Type: Article

References (31)

1. Birney,E. (2011) Assemblies: the good, the bad, the ugly. Nat. Methods, 8, 59-60.
2. Cock,P.J. et al. (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38, 1767-1771.
3. Durbin,R.M. et al.; 1000 Genomes Project Consortium. (2010)Amap of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
4. Edgar,R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
5. Fritz,M.H.Y. et al. (2011) Efficient storage of high throughput sequencing data using reference-based compression. Genome Res., 21, 734-740.
6. Hazelhurst,S. et al. (2008) An overview of the wcd EST clustering tool. Bioinformatics, 24, 1542.
7. Holt,R.A. and Jones,S.J. (2008) The new paradigm of flow cell sequencing. Genome Res., 18, 839-846.
8. Hsieh,L.C. et al. (2009) Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol., 151, 2120-2132.
9. Huang,X. and Madan,A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868.
10. Jiang,H. and Wong,W. (2008) Seqmap: mapping massive amount of oligonucleotides to the genome. Bioinformatics, 24, 2395.
11. Jiao,Y. and Meyerowitz,E.M. (2010) Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol. Syst. Biol., 6, 419-419.
12. Johnson,C. et al. (2009) Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res., 19, 1429-1440.
13. Jothi,R. et al. (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res., 36, 5221-5231.
14. Kaufmann,K. et al. (2010) Orchestration of floral initiation by APETALA1. Science, 328, 85-89.
15. Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, 25-34.
16. Leinonen,R. et al. (2010) The European Nucleotide Archive. Nucleic Acids Res., 39, 28-31.
17. Li,W. and Godzik,A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
18. Li,H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851.
19. Li,H. and Durbin,R. (2009a) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
20. Li,H. et al.; 1000 Genome Project Data Processing Subgroup (2009b) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
21. Lin,H. et al. (2008) ZOOM! Zillions of oligos mapped. Bioinformatics, 24, 2431-2437.
22. Ma,B. et al. (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics, 18, 440-445.
23. Medini,D. et al. (2008) Microbiology in the post-genomic era. Nat. Rev. Microbiol., 6, 419-430.
24. Miller,J.R. et al. (2010) Assembly algorithms for next-generation sequencing data. Genomics, 95, 315-327.
25. Montgomery,T.A. et al. (2008) AGO1-miR173 complex initiates phased siRNA formation in plants. Proc. Natl Acad. Sci. USA, 105, 20055-20062.
26. Picardi,E. et al. (2009) EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data. BMC Bioinformatics, 10 (Suppl. 6), S10.
27. Qu,W. et al. (2009). Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res, 19, 1309-1315.
28. Rao,D. et al. (2010) PEACE: Parallel Environment for Assembly and Clustering of Gene Expression. Nucleic acids research, 38 (Suppl. 2), W737.
29. Schmidt,B. et al. (2009) A fast hybrid short read fragment assembly algorithm. Bioinformatics, 25, 2279-2280.
30. Warren,R.L. et al. (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics, 23, 500-501.
31. Zerbino,D.R. and Birney,E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res, 18, 821-829.