ConDeTri - a content dependent read trimmer for illumina data

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Smeds, Linnéa ^a   Künstner, Axel ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; CONTENT DEPENDENT TRIMMING; CONTROLLED STUDY; DATA ANALYSIS; DNA CONTENT; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENE MAPPING; GENE SEQUENCE; GENOME SIZE; HETEROZYGOSITY; INFORMATION PROCESSING; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; DNA SEQUENCE; METHODOLOGY;

SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 80054784996     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026314     Document Type: Article

References (27)

1. Sanger F, Nicklen S, Coulson AR, (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467.
2. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends in Genetics 24: 133-141.
3. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
4. Dohm JC, Lottaz C, Borodina T, Himmelbauer H, (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research 36: e105-e105.
5. Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, et al. (2009) Sequence assembly. Computational Biology and Chemistry 33: 121-136.
6. Pevzner P, Tang H, Waterman M, (2001) An Eulerian path approach to DNA fragment assembly. PNAS 98: 9748-9753.
7. Zerbino D, Birney E, (2008) Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs. Genome Research gr.074492.074107-.
8. Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20: 265-272.
9. Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, et al. (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24: 2818-2824.
10. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
11. Cox MP, Peterson DA, Biggs PJ, (2010) SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11: 485.
12. Dohm JC, Lottaz C, Borodina T, Himmelbauer H, (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research gr.6435207-.
13. Kelley DR, Schatz MC, Salzberg SL, (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biology 11: R116.
14. Salmela L, (2010) Correction of sequencing errors in a mixed set of reads. Bioinformatics 26: 1284-1290.
15. Schröder J, Schröder H, Puglisi SJ, Sinha R, Schmidt B, (2009) SHREC: a short-read error correction method. Bioinformatics 25: 2157-2163.
16. Ilie L, Fazayeli F, Ilie S, (2011) HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 27: 295-302.
17. Ye L, Hillier LW, Minx P, Thane N, Locke D, et al. (2011) A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biology 12: R31.
18. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, et al. (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nature Methods 6: 291-295.
19. Li R, Fan W, Tian G, Zhu H, He L, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.
20. Miller J, Koren S, Sutton G, (2010) Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
21. Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W, (2010) Calling SNPs without a reference sequence. BMC Bioinformatics 11: 130.
22. Bwa website. Available: http://bio-bwa.sourceforge.net/. Accessed 2011 Sept 27.
23. Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12.
24. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 25: 1754-1760.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 25: 2078-2079.
26. ICGC (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432: 717-722.
27. Gregory TR, (2005) Synergy between sequence and size in Large-scale genomics. Nat Rev Genet 6: 699-708.