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Implements an algorithm for whole genome assembly of deep paired-end short reads. Meraculous relies on an efficient and conservative traversal of a subgraph of the k-mer de Bruijn graph (DBG) of oligonucleotides with unique high quality extensions in the dataset. Unlike other short-read assemblers, Meraculous avoids an explicit error correction step, instead relying on base quality scores. Meraculous also incorporates a low-memory hash structure to access the DBG, allowing a small memory footprint compared with other short-read assemblers. Using Meraculous, it was shown that high quality, near-complete de novo assemblies of small fungal genomes can be produced using deep short-read paired-end datasets.

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Meraculous classification

Meraculous specifications

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Command line interface
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GNU General Public License version 3.0

Meraculous distribution


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Meraculous support


  • Eugene Goltsman <>
  • Jarrod Chapman <>

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U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; Illumina, Inc., Hayward, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA

Funding source(s)

This work was performed under the auspices of the U.S. Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, and at the Center for Integrative Genomics at UC Berkeley supported by a grant from the Gordon and Betty Moore Foundation.

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