ALLPATHS swMATH ID: 6112 Software Authors: J.Butler,I.MacCallum,M.Kleber,I.A.Shlyakhter,M.K.Belmonte,E.S.Lander, C. Nusbaum, D. B. Jaffe Description: 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. Homepage: http://genome.cshlp.org/content/18/5/810.short Operating Systems: Installed on blacklight. Related Software: Velvet; SHARCGS; GAGE; BLAT; ABySS; ARACHNE; QSRA; SOAPdenovo; SPAdes; SSAKE; SHREC; Reptile; HiTEC; Quake; BLASTZ; Cytoscape; Rfam; SHRiMP; KEGG; IDBA Cited in: 10 Publications all top 5 Cited by 40 Authors 2 Iliopoulos, Costas S. 2 Kundu, Ritu 2 Mohamed, Manal 2 Vayani, Fatima 1 Aleksandrov, A. V. 1 Aransay, Ana M. 1 Błażewicz, Jacek 1 Branković, Ljiljana 1 Brown, C. Titus 1 Canino-Koning, Rosangela 1 Frohmberg, Wojciech 1 Hackenberg, Michael 1 Hintze, Arend 1 Howe, Adina 1 Jean, Géraldine 1 Kasprzak, Marta 1 Kazakov, S. V. 1 Keith, Jonathan M. 1 Kierzynka, Michal 1 Li, Yong 1 Liu, Fayao 1 Pell, Jason 1 Pissis, Solon P. 1 Radulescu, Andreea 1 Richard, Hugues 1 Rodríguez-Ezpeleta, Naiara 1 Rusu, Irena 1 Schulz, Marcel H. 1 Sergushichev, Alexey A. 1 Shalyto, A. A. 1 Świercz, Aleksandra 1 Tiedje, James M. 1 Tsarev, F. N. 1 Weese, David 1 Wojciechowski, Paweł T. 1 Xiong, Wei 1 Yin, Jianping 1 Zhan, Yubin 1 Zhao, Zhiheng 1 Zurkowski, Piotr Cited in 5 Serials 1 Theoretical Computer Science 1 European Journal of Operational Research 1 Proceedings of the National Academy of Sciences of the United States of America 1 Izvestiya Saratovskogo Universiteta. Novaya Seriya. Seriya Matematika, Mekhanika, Informatika 1 Methods in Molecular Biology Cited in 4 Fields 10 Biology and other natural sciences (92-XX) 6 Computer science (68-XX) 4 Combinatorics (05-XX) 2 General and overarching topics; collections (00-XX) Citations by Year