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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 (deBruijn) graph 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 novel low-memory hash structure to access the deBruijn graph, allowing a small memory footprint compared with other short-read assemblers.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Biological technology:
Illumina
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
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Institution(s)

U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, 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.

  • (Chapman et al., 2011) Meraculous: de novo genome assembly with short paired-end reads. PloS one.
    PMID: 21876754
  • (Magoc et al., 2013) GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics.
    PMID: 23665771
  • (Miller et al., 2010) Assembly algorithms for next-generation sequencing data. Genomics.
    PMID: 20211242
  • (Narzisi and Mishra, 2011) Comparing de novo genome assembly: the long and short of it. PloS one.
    PMID: 21559467
  • (Henson et al., 2012) Next-generation sequencing and large genome assemblies. Pharmacogenomics.
    PMID: 22676195
  • (Kleftogiannis et al., 2013) Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PloS one.
    PMID: 24086547
  • (Nagarajan and Pop, 2013) Sequence assembly demystified. Nature reviews Genetics.
    PMID: 23358380
  • (Bradnam et al., 2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience.
    PMID: 23870653
  • (Salzberg et al., 2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome research.
    PMID: 22147368
  • (Utturkar et al., 2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics.
    PMID: 24930142
  • (Alkan et al., 2011) Limitations of next-generation genome sequence assembly. Nature methods.
    PMID: 21102452
  • (Love et al., 2016) Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC genomics.
    PMID: 26944054

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