ALLPATHS

ALLPATHS-LG is a whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads ( 100bp) such as those produced by the new generation of sequencers. The significant difference between ALLPATHS and traditional assemblers such as Arachne is that ALLPATHS assemblies are not necessarily linear, but instead are presented in the form of a graph. This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies. (Source: http://www.psc.edu/)


References in zbMATH (referenced in 13 articles )

Showing results 1 to 13 of 13.
Sorted by year (citations)

  1. Blazewicz, Jacek; Kasprzak, Marta; Kierzynka, Michal; Frohmberg, Wojciech; Swiercz, Aleksandra; Wojciechowski, Pawel; Zurkowski, Piotr: Graph algorithms for DNA sequencing -- origins, current models and the future (2018)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  3. Brankovic, Ljiljana; Iliopoulos, Costas S.; Kundu, Ritu; Mohamed, Manal; Pissis, Solon P.; Vayani, Fatima: Linear-time superbubble identification algorithm for genome assembly (2016)
  4. Iliopoulos, Costas S.; Kundu, Ritu; Mohamed, Manal; Vayani, Fatima: Popping superbubbles and discovering clumps: recent developments in biological sequence analysis (2016)
  5. Sergushichev, A. A.; Aleksandrov, A. V.; Kazakov, S. V.; Tsarev, F. N.; Shalyto, A. A.: Combining de Bruijn graphs, overlap graphs and microassembly for \textitdenovo genome assembly (2013)
  6. Pell, Jason; Hintze, Arend; Canino-Koning, Rosangela; Howe, Adina; Tiedje, James M.; Brown, C. Titus: Scaling metagenome sequence assembly with probabilistic de Bruijn graphs (2012)
  7. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  8. Zhao, Zhiheng; Yin, Jianping; Zhan, Yubin; Xiong, Wei; Li, Yong; Liu, Fayao: PSAEC: an improved algorithm for short read error correction using partial suffix arrays (2011)
  9. Kingsford, Carl; Schatz, Michael C.; Pop, Mihai: Assembly complexity of prokaryotic genomes using short reads (2010) ioport
  10. Palmer, Lance E.; Dejori, Mathäus; Bolanos, Randall A.; Fasulo, Daniel P.: Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction (2010) ioport
  11. Ratan, Aakrosh; Zhang, Yu; Hayes, Vanessa M.; Schuster, Stephan C.; Miller, Webb: Calling SNPs without a reference sequence (2010) ioport
  12. Jr., Douglas W. Bryant; Wong, Weng-Keen; Mockler, Todd C.: QSRA - a quality-value guided \textitdenovoshort read assembler (2009) ioport
  13. Wooley, John C.; Ye, Yuzhen: Metagenomics: facts and artifacts, and computational challenges (2009) ioport