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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


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Publication for Meraculous

Meraculous citations


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

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

[…] protocol: kapa stranded mrna-seq kit for illumina® platform (kr0960 -v3.15) and sequenced on an illumina hiseq 2500 (108 × 150 bp reads). greater than 80% of the transcriptome reads mapped to the meraculous assembly., meraculous is a whole genome assembler for next generation sequencing data geared for large genomes []. the guayule genome was first assembled using the mercaculous assembler […]


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

PMCID: 5553748
PMID: 28797224
DOI: 10.1186/s12864-017-3952-7

[…] 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 […]


Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula

PMCID: 5545040
PMID: 28778149
DOI: 10.1186/s12864-017-3971-4

[…] putative chimeric sequences were broken. an iterative approach was taken by feeding the resulting scaffolds back into the pipeline. refinement of local ordering and orientation and gap closing using meraculous’s marauder module was done at the end []., five grams of young leaf tissue was obtained from greenhouse-grown plants dark-treated for 24 h before harvest. high molecular weight dna […]


Complete Genome Sequence of Streptomyces sp. Sge12, Which Produces Antibacterial and Fungicidal Activities

PMCID: 5477408
PMID: 28546495
DOI: 10.1128/genomeA.00415-17

[…] coverage) and single-molecule real-time pacbio rsii (1,127.1-mb sequences, 139.0-fold coverage) sequencing. the reads from the illumina hiseq 4000 and pacbio rsii sequencing were assembled using meraculous version 2.0 software () and rs_hgap assembly version 3.0 software (), respectively. subsequently, the final assembly of the whole genome was finished by using illumina/pacbio hybrid […]


Draft Genome Sequence of Tritrichomonas foetus Strain K

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., automate […]


Positional bias in variant calls against draft reference assemblies

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

[…] 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 […]

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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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