MaSuRCA pipeline

MaSuRCA specifications


Unique identifier OMICS_00020
Name MaSuRCA
Alternative name Maryland Super-Read Celera Assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Steven Salzberg <>
  • person_outline Aleksey Zimin <>

Publication for Maryland Super-Read Celera Assembler


The MaSuRCA genome assembler.

2013 Bioinformatics
PMCID: 3799473
PMID: 23990416
DOI: 10.1093/bioinformatics/btt476

MaSuRCA IN pipelines

PMCID: 5759298
PMID: 29310588
DOI: 10.1186/s12864-017-4403-1

[…] from the hiseq2500 in fastq format were used for the assembly. prior to assembly, fastqc ( was run to verify the quality of the reads. masurca assembler (version 2.3.2) [32] was used to assemble the raw data into 98,162 scaffolds and has been deposited at ddbj/ena/genbank under the accession peqf00000000. to obtain a more reasonable […]

PMCID: 5454193
PMID: 28572310
DOI: 10.1128/genomeA.00405-17

[…] data for high-quality vector- and adaptor-free reads for genome assembly (cutoff read length for high quality, 80%; cutoff quality score, 20). high-quality vector-filtered reads were assembled with masurca (13), under the default parameter predicted by the assembler for each genome, and annotated with the help of the rapid annotations using subsystems technology (rast) (14). table 1 summarizes […]

PMCID: 5677167
PMID: 28963165
DOI: 10.1534/g3.117.300107

[…] assemblies using illumina data and nanopore data separately, and using different assembly programs [megahit (li et al. 2015), spades (bankevich et al. 2012), sspace (boetzer et al. 2011), and masurca (bosi et al. 2015)]. the figures demonstrate that the illumina-only assembly is more complete although far more fragmented than the nanopore-only assembly. the hybrid assembly combines […]

PMCID: 3907721
PMID: 24482506
DOI: 10.1128/genomeA.00004-14

[…] data and 709,435 paired reads, and (iii) a roche gs flx 8-kb-long paired-end technology generating 103,198 reads with 35,043,425 bp of a raw sequence. de novo hybrid assembly was performed using the masurca genome assembler version 2.1.0 (7), resulting in 5 scaffolds of >1,000 bp. gaps were initially filled in silico using the gapfiller software version 1.3 (8), and the remaining gaps […]

PMCID: 4038898
PMID: 24874663
DOI: 10.1128/genomeA.00530-14

[…] coverage of 212-fold. reads were filtered and trimmed with qc toolkit (7), and redundancies were removed using trinity in silico normalization (8). the processed reads were then assembled using masurca (9) (cgwerrorrate=0.15, insert size=900). based on reciprocal blastn (10), redundant contigs (those included in a bigger read) were removed. a final assembly of 277 contigs (>500 pb) […]

MaSuRCA institution(s)
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Physical Sciences and Technology, University of Maryland, College Park, MD, USA; Department of Plant Sciences, University of California, Davis, CA, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA; Departments of Mathematics and Physics, University of Maryland, College Park, MD, USA; Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
MaSuRCA funding source(s)
Supported in part by National Science Foundation (NSF) grant IOS-1238231, by National Institutes of Health (NIH) grant R01- HG006677, and by the Intramural Research Program of the National Human Genome Research Institute, NIH.

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