第5章

参考文献：第5章 小片段序列组装


Bryant, D. W., Jr., et al. 2009. QSRA: a quality-value guided de novo short read assembler. BMC Bioinformatics. 10: 69. [PubMed]

Butler, J., et al. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18(5): 810-820. [PubMed]

Chaisson, M. J. and P. A. Pevzner. 2008. Short read fragment assembly of bacterial genomes. Genome Res. 18(2): 324-330. [PubMed]

Diguistini, S., et al. 2009. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol. 10(9): R94. [PubMed]

Dohm, J. C., et al. 2007. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 17(11): 1697-1706. [PubMed]

Farrer, R. A., et al. 2009. De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett. 291(1): 103-111. [PubMed]

Gnerre, S., et al. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 108(4): 1513-1518. [PubMed]

Hernandez, D., et al. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18(5): 802-809. [PubMed]

Hossain, M. S., et al. 2009. Crystallizing short-read assemblies around seeds. BMC Bioinformatics. 10 Suppl 1: S16. [PubMed]

Huang, X. and A. Madan. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9(9): 868-877. [PubMed]

Jeck, W. R., et al. 2007. Extending assembly of short DNA sequences to handle error. Bioinformatics. 23(21): 2942-2944. [PubMed]

Kingsford, C., et al. 2010. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics. 11: 21. [PubMed]

Kumar, S. and M. L. Blaxter. 2010. Comparing de novo assemblers for 454 transcriptome data. BMC Genomics. 11: 571. [PubMed]

Li, R., et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature. 463(7279): 311-317. [PubMed]

Li, R., et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20(2): 265-272. [PubMed]

Lin, Y., et al. 2011. Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics. 27(15): 2031-2037. [PubMed]

Margulies, M., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437(7057): 376-380. [PubMed]

Miller, J. R., et al. 2008. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics. 24(24): 2818-2824. [PubMed]

Miller, J. R., et al. 2010. Assembly algorithms for next-generation sequencing data. Genomics. 95(6): 315-327. [PubMed]

Reinhardt, J. A., et al. 2009. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 19(2): 294-305. [PubMed]

Schmidt, B., et al. 2009. A fast hybrid short read fragment assembly algorithm. Bioinformatics. 25(17): 2279-2280. [PubMed]

Simpson, J. T., et al. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19(6): 1117-1123. [PubMed]

Surget-Groba, Y. and J. I. Montoya-Burgos. 2010. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 20(10): 1432-1440. [PubMed]

Warren, R. L., et al. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23(4): 500-501. [PubMed]

Zerbino, D. R. and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18(5): 821-829. [PubMed]

Zhang, W., et al. 2011. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One. 6(3): e17915. [PubMed]