Filtering duplicate reads from 454 pyrosequencing data

Bioinformatics

Volumn 29, Issue 7, 2013, Pages 830-836

  Balzer, Susanne ^a,b   Malde, Ketil ^a   Grohme, Markus A ^c   Jonassen, Inge ^b,d  

^a INSTITUTE OF MARINE RESEARCH   (Norway)

^b UNIVERSITY OF BERGEN   (Norway)

^c TECHNICAL UNIVERSITY OF APPLIED SCIENCES WILDAU   (Germany)

^d Uni Computing   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; CHROMOSOME MAP; COMPUTER PROGRAM; DNA SEQUENCE; METAGENOMICS; METHODOLOGY;

ALGORITHMS; BAYES THEOREM; CHROMOSOME MAPPING; METAGENOMICS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84875609855     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt047     Document Type: Article

References (39)

1. Balzer, S. et al. (2010) Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics, 26, i420-i425.
2. Briggs, A.W. et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA, 104, 14616-14621.
3. Cahill, M.J. et al. (2010) Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies. PLoS One, 5, e11518.
4. Chou, H.H. and Holmes, M.H. (2001) DNA sequence quality trimming and vector removal. Bioinformatics, 17, 1093-1104.
5. Darling, A.E. et al. (2011) Mauve assembly metrics. Bioinformatics, 27, 2756-2757.
6. Dong, H. et al. (2011) Artificial duplicate reads in sequencing data of 454 Genome Sequencer FLX System. Acta Biochim. Biophys. Sin. (Shanghai), 43, 496-500.
7. Ewing, B. et al. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res, 8, 175-185.
8. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res, 8, 186-194.
9. Falgueras, J. et al. (2010) SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinformatics, 11, 38.
10. Gilles, A. et al. (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 12, 245.
11. Gomez-Alvarez, V. et al. (2009) Systematic artifacts in metagenomes from complex microbial communities. ISME J., 3, 1314-1317.
12. Houseley, J. and Tollervey, D. (2010) Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS One, 5, e12271.
13. Huse, S.M. et al. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol., 8, R143.
14. Kanagawa, T. (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng., 96, 317-323.
15. Kong, Y. (2011) Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics, 98, 152-153.
16. Kuhl, H. et al. (2010) The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics, 11, 68.
17. Kunin, V. et al. (2009) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol., 12, 118-123.
18. Leamon, J.H. et al. (2003) A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis, 24, 3769-3777.
19. Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
20. Li, W. et al. (2012) Ultrafast clustering algorithms for metagenomic sequence analysis. Brief. Bioinform., 13, 656-668.
21. 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.
22. Loman, N.J. et al. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol., 30, 434-439.
23. Malde, K. et al. (2006) RBR: library-less repeat detection for ESTs. Bioinformatics, 22, 2232-2236.
24. Margulies, M. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
25. Mariette, J. et al. (2011) Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool. BMC Res. Notes, 4, 149.
26. Niu, B. et al. (2010) Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics, 11, 187.
27. Phillippy, A.M. et al. (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol., 9, R55.
28. Quince, C. et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods, 6, 639-641.
29. Quince, C. et al. (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12, 38.
30. Quinlan, A.R. et al. (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat. Methods, 5, 179-181.
31. Roche Applied Science. (2008) Genome Sequencer Data Analysis SoftwareManual, Software Version 2.0.00. Roche Diagnostics GmbH.
32. Sanger, F. et al. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
33. Sogin, M.L. et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere. Proc. Natl Acad. Sci. USA, 103, 12115-12120.
34. Tawfik, D.S. and Griffiths, A.D. (1998) Man-made cell-like compartments for molecular evolution. Nat. Biotechnol., 16, 652-656.
35. Teal, T.K. and Schmidt, T.M. (2010) Identifying and removing artificial replicates from 454 pyrosequencing data. Cold Spring Harb. Protoc., 2010, pdb.prot5409.
36. Vacic, V. et al. (2008) A probabilistic method for small RNA flowgram matching. Pac. Symp. Biocomput., 2008, 75-86.
37. White, J.R. et al. (2008) Figaro: a novel statistical method for vector sequence removal. Bioinformatics, 24, 462-467.
38. Williams, R. et al. (2006) Amplification of complex gene libraries by emulsion PCR. Nat. Methods, 3, 545-550.
39. Zheng, Z. et al. (2010) Titration-free massively parallel pyrosequencing using trace amounts of starting material. Nucleic Acids Res., 38, e137.