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Volumn 28, Issue 11, 2012, Pages 1420-1428

IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BACTERIUM; DNA SEQUENCE; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; METHODOLOGY; SINGLE CELL ANALYSIS;

EID: 84861760530     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts174     Document Type: Article
Times cited : (2314)

References (20)
  • 1
    • 43149086380 scopus 로고    scopus 로고
    • ALLPATHS: de novo assembly of whole-genome shotgun microreads
    • Butler, J. et al. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820.
    • (2008) Genome Res , vol.18 , pp. 810-820
    • Butler, J.1
  • 2
    • 39049156065 scopus 로고    scopus 로고
    • Short read fragment assembly of bacterial genomes
    • Chaisson, M.J. and Pevzner, P.A. (2008) Short read fragment assembly of bacterial genomes. Genome Res., 18, 324-330.
    • (2008) Genome Res , vol.18 , pp. 324-330
    • Chaisson, M.J.1    Pevzner, P.A.2
  • 3
    • 59949093527 scopus 로고    scopus 로고
    • De novo fragment assembly with short mate-paired reads: Does the read length matter?
    • Chaisson, M.J. et al. (2009) De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res., 19, 336-346.
    • (2009) Genome Res , vol.19 , pp. 336-346
    • Chaisson, M.J.1
  • 4
    • 80054732674 scopus 로고    scopus 로고
    • Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
    • Chitsaz, H. et al. (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol., 29, 915-921.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 915-921
    • Chitsaz, H.1
  • 5
    • 83055181941 scopus 로고    scopus 로고
    • Assemblathon 1 a competitive assessment of de novo short read assembly methods
    • Earl, D. et al. (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res., 21, 2224-2241.
    • (2011) Genome Res , vol.21 , pp. 2224-2241
    • Earl, D.1
  • 6
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
    • Hernandez, D. et al. (2008) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res., 18, 802-809.
    • (2008) Genome Res , vol.18 , pp. 802-809
    • Hernandez, D.1
  • 7
    • 78649358717 scopus 로고    scopus 로고
    • Quake: quality-aware detection and correction of sequencing errors
    • Kelley, D.R. et al. (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol., 11, R116.
    • (2010) Genome Biol , vol.11
    • Kelley, D.R.1
  • 8
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 9
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-272.
    • (2010) Genome Res , vol.20 , pp. 265-272
    • Li, R.1
  • 10
    • 79959485321 scopus 로고    scopus 로고
    • Error correction of high-throughput sequencing datasets with non-uniform coverage
    • Medvedev, P. et al. (2011) Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics, 27, i137-i141.
    • (2011) Bioinformatics , vol.27
    • Medvedev, P.1
  • 11
    • 59149090570 scopus 로고    scopus 로고
    • MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
    • Noguchi, H. et al. (2008) MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res., 15, 387-396.
    • (2008) DNA Res , vol.15 , pp. 387-396
    • Noguchi, H.1
  • 12
    • 84872207312 scopus 로고    scopus 로고
    • IDBA - a practical iterative de Bruijn graph de novo assembler
    • Peng, Y. et al. (2010) IDBA - a practical iterative de Bruijn graph de novo assembler. In RECOMB, Lisbon.
    • (2010) RECOMB, Lisbon
    • Peng, Y.1
  • 13
    • 79959422558 scopus 로고    scopus 로고
    • Meta-IDBA: a de Novo assembler for metagenomic data
    • Peng, Y. et al. (2011) Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics, 27, i94-i101.
    • (2011) Bioinformatics , vol.27
    • Peng, Y.1
  • 14
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • Pevzner, P.A. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748-9753.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 9748-9753
    • Pevzner, P.A.1
  • 15
    • 70149108769 scopus 로고    scopus 로고
    • Whole genome amplification and de novo assembly of single bacterial cells
    • Rodrigue, S. et al. (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLoS One, 4, e6864.
    • (2009) PLoS One , vol.4
    • Rodrigue, S.1
  • 16
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: a parallel assembler for short read sequence data
    • Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
    • (2009) Genome Res , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 17
    • 77649200259 scopus 로고    scopus 로고
    • Aprimer on metagenomics
    • Wooley, J.C. et al. (2010)Aprimer on metagenomics. PLoS Comput. Biol., 6, e1000667.
    • (2010) PLoS Comput. Biol. , vol.6
    • Wooley, J.C.1
  • 18
    • 65449134335 scopus 로고    scopus 로고
    • Assembling the marine metagenome, one cell at a time
    • Woyke, T. et al. (2009) Assembling the marine metagenome, one cell at a time. PLoS One, 4, e5299.
    • (2009) PLoS One , vol.4
    • Woyke, T.1
  • 19
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 20
    • 77949511368 scopus 로고    scopus 로고
    • Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
    • Zerbino, D.R. et al. (2009) Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One, 4, e8407.
    • (2009) PLoS One , vol.4
    • Zerbino, D.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.