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Method: Scaffolding a Caenorhabditis nematode genome with RNA-seq
- Ali Mortazavi,
- Erich M. Schwarz,
- Brian Williams,
- Lorian Schaeffer,
- Igor Antoshechkin,
- Barbara J. Wold,
- and Paul W. Sternberg
Genome Res. December 2010 20: 1740-1747; Published in Advance October 27, 2010, doi:10.1101/gr.111021.110
.... Proc Natl Acad Sci 105: 14802–14807. Pop M, Kosak DS, Salzberg SL. 2004. Hierarchical scaffolding with Bambus. Genome Res 14: 149–159. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. 2010. JASPAR 2010: The greatly expanded open...
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Method: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
- Sergey Koren,
- Brian P. Walenz,
- Konstantin Berlin,
- Jason R. Miller,
- Nicholas H. Bergman,
- and Adam M. Phillippy
Genome Res. May 2017 27: 722-736; Published in Advance March 15, 2017, doi:10.1101/gr.215087.116
...assembly (GFA) format for analysis or integration with complementary phasing and scaffolding techniques. The combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex s. [Supplemental material is available...
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Resource: Efficient de novo assembly of large genomes using compressed data structures
- Jared T. Simpson and
- Richard Durbin
Genome Res. March 2012 22: 549-556; Published in Advance December 7, 2011, doi:10.1101/gr.126953.111
...the compressed Burrows-Wheeler transform, and a new assembler based on these called SGA ( S tring G raph A ssembler). We describe algorithms to error-correct, assemble, and scaffold large sets of sequence data. SGA uses the overlap-based string graph model of assembly, unlike most de novo assemblers that rely...
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Methods: Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
- Jade P. Vinson,
- David B. Jaffe,
- Keith O'Neill,
- Elinor K. Karlsson,
- Nicole Stange-Thomann,
- Scott Anderson,
- Jill P. Mesirov,
- Nori Satoh,
- Yutaka Satou,
- Chad Nusbaum,
- Bruce Birren,
- James E. Galagan,
- and Eric S. Lander
Genome Res. August 2005 15: 1127-1135; doi:10.1101/gr.3722605
...that the sequenced individual had an extremely high heterozygosity rate, averaging 4.6% with significant regional variation and rearrangements at all physical scales. Applied to these data, our method produced a reference assembly covering 157 Mb, with N50 contig and scaffold sizes of 47 kb and 989 kb, respectively...
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Letter: Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production
- Juan Lucas Argueso,
- Marcelo F. Carazzolle,
- Piotr A. Mieczkowski,
- Fabiana M. Duarte,
- Osmar V.C. Netto,
- Silvia K. Missawa,
- Felipe Galzerani,
- Gustavo G.L. Costa,
- Ramon O. Vidal,
- Melline F. Noronha,
- Margaret Dominska,
- Maria G.S. Andrietta,
- Sílvio R. Andrietta,
- Anderson F. Cunha,
- Luiz H. Gomes,
- Flavio C.A. Tavares,
- André R. Alcarde,
- Fred S. Dietrich,
- John H. McCusker,
- Thomas D. Petes,
- and Gonçalo A.G. Pereira
Genome Res. December 2009 19: 2258-2270; Published in Advance October 7, 2009, doi:10.1101/gr.091777.109
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ARTICLE: Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects
- Patrick H. Degnan,
- Adam B. Lazarus,
- and Jennifer J. Wernegreen
Genome Res. August 2005 15: 1023-1033; doi:10.1101/gr.3771305
...of the 30S and 50S ribosomal subunits ( Wimberly et al. 2000 ; Harms et al. 2001 ). These subunits assemble from 52 ribosomal proteins that form scaffolds around the 5S, 16S, and 23S ribosomal RNAs. Notably, many of the genes that show elevated substitution rates are positioned at the periphery...
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Methods: De Novo Repeat Classification and Fragment Assembly
- Paul A. Pevzner,
- Haixu Tang,
- and Glenn Tesler
Genome Res. September 2004 14: 1786-1796; doi:10.1101/gr.2395204

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