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We present Meraculous2, an update to the Meraculous short-read assembler thatincludes (1) handling of allelic variation using "bubble" structures within thede Bruijn graph, (2) improved gap closing, and (3) an improved scaffoldingalgorithm that produces more complete assemblies without compromisingscaffolding accuracy. The speed and bandwidth efficiency of the new parallelimplementation have also been substantially improved, allowing the assembly ofa human genome to be accomplished in 24 hours on the JGI/NERSC Genepool system.To highlight the features of Meraculous2 we present here the assembly of thediploid human genome NA12878, and compare it with previously publishedassemblies of the same data using other algorithms. The Meraculous2 assembliesare shown to have better completeness, contiguity, and accuracy than otherpublished assemblies for these data. Practical considerations includingpre-assembly analyses of polymorphism and repetitiveness are described.

Meraculous2: fast accurate short-read assembly of large polymorphic genomes