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Meraculous specifications


Unique identifier OMICS_00021
Name Meraculous
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.2.5
Stability Stable
Maintained Yes




No version available


  • person_outline Eugene Goltsman
  • person_outline Jarrod Chapman

Additional information

Publication for Meraculous

Meraculous citations


Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes

BMC Genomics
PMCID: 5907723
PMID: 29673330
DOI: 10.1186/s12864-018-4653-6

[…] equencing, assembly and annotation of the guayule genome was undertaken to promote the application of current molecular and breeding tools improvement efforts. While fragmented (260 k Scaffolds), the Meraculous assembly reported here is essentially complete allowing, for identification and utilization of specific genes and gene components, as well as contributing to the development of molecular br […]


The adaptive landscape of wildtype and glycosylation deficient populations of the industrial yeast Pichia pastoris

BMC Genomics
PMCID: 5553748
PMID: 28797224
DOI: 10.1186/s12864-017-3952-7
call_split See protocol

[…] t detection, was obtained through de-novo assembly and grouping of the assembled scaffolds into chromosomes by mapping them on the CBS 7435 reference strain []. De-novo assembly was accomplished with Meraculous []. Input data consisted of 4,048,141 quality trimmed reads with an average read length of 260.48 bp and a mean quality Phred score of 34.0. The final assembly consisted of 48 scaffolds wit […]


Draft Genome Sequence of Tritrichomonas foetus Strain K

Genome Announc
PMCID: 5399258
PMID: 28428299
DOI: 10.1128/genomeA.00195-17

[…] 2,157 bp. The longest scaffold was 694,095 bp. AllPaths-LG estimated the genome size to be 161,213,455 bp, with 62% repetitive sequences. To improve the assembly, several softwares were used, such as Meraculous, Ray, SOAPdenovo, and SPAdes. The results were similar to those found using the AllPaths software. The number of repeated sequences makes it impossible to assemble larger contigs.Automated […]


Positional bias in variant calls against draft reference assemblies

BMC Genomics
PMCID: 5368935
PMID: 28351369
DOI: 10.1186/s12864-017-3637-2

[…] erlaps between k-mers that are k−1 bases long become edges. Among the assemblers that implement the string graph approach are SGA [] and SAGE [] while de Bruijn graphs are incorporated into ABySS [], Meraculous [], ALLPATHS-LG [], and SOAPdenovo2 [] among many others.Pipeline for genome assembly normally includes a rigorous error correction of the reads, which can be done either before the assembl […]


Implications of evolutionary engineering for growth and recombinant protein production in methanol based growth media in the yeast Pichia pastoris

Microb Cell Fact
PMCID: 5356285
PMID: 28302114
DOI: 10.1186/s12934-017-0661-5
call_split See protocol

[…] Eurofins Genomics (Eurofins Genomics NGS laboratory, Ebersberg, Germany). Cutadapt [] was used for adapter-removal and quality filtering of the reads. For the genome assembly of the ancestral strain, Meraculous was applied []. The final assembly of the ancestral strain consisted of 48 scaffolds with a total of 9,310,711 bp and a N50 score of 910,678. Out of 4,048,141 quality trimmed input reads wi […]


A whole genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Genome Biol
PMCID: 4373400
PMID: 25637298
DOI: 10.1186/s13059-015-0582-8

[…] All contigs ≥1 kbp of the IWGSC assembly of cv. Chinese Spring were aligned against all meraculous scaffolds of W7984 with megablast []. Only HSPs longer than 500 bp and sequence identity ≥98.5% were considered. The longest HSP of each IWGSC contig was used to assign it to a meraculous s […]


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Meraculous institution(s)
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
Meraculous funding source(s)
Supported by the U.S. Department of Energy’s Office of Science, Biological and Environmental Research Program, the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, and the Center for Integrative Genomics at UC Berkeley funded by a grant from the Gordon and Betty Moore Foundation.

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