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
Referenced in: 10 Publications

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