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Opera specifications


Unique identifier OMICS_00045
Name Opera
Alternative names Optimal Paired-End Read Assembler, OPERA-LG
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Paired-end/mate-pair reads
Output data Scaffolds
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Song Gao <>

Publications for Optimal Paired-End Read Assembler

Opera citations


Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut

PMCID: 5862939
PMID: 29435649
DOI: 10.1007/s00792-018-1011-1

[…] were trimmed using trimmomatic (lohse et al. ), then assembled thought spades software (nurk et al. ; bankevich et al. ). contigs obtained were combined together by sspace (boetzer et al. ) and opera software (gao et al. ) helped by gapfiller (boetzer and pirovano ) to reduce the set. some manual refinements using clc genomics v7 software (clc bio, aarhus, denmark) and homemade tools […]


Draft Genome Sequence of Singapore Klebsiella pneumoniae subsp. pneumoniae Isolate DS32358_14, Which Contains the Carbapenemase Gene blaVIM 1

PMCID: 5754483
PMID: 29301903
DOI: 10.1128/genomeA.01377-17

[…] this library was sequenced on an illumina hiseq4000 machine with 2 × 150-bp reads. the data were assembled using velvet (version 1.2.10) () with a minimum contig cutoff of 500 bp, scaffolded with opera (version 1.4.1) (), and finished with finis (version 0.3) (). in total, 4,346,527 paired-end reads passed filtering, representing an approximate coverage of 200× (based on the final assembly)., […]


Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach

PMCID: 5723288
PMID: 29259619
DOI: 10.3389/fgene.2017.00180

[…] using platanus in scaffolding mode. these paired-end reads, and mate-pair libraries were used again to close the gap using platanus in gap close mode. the obtained scaffolds were optimized using opera (ver. 1.3.1) (gao et al., ) to improve the assembly quality and produced a 340.0 mbp assembled sequence. we further attempted to close the gap in the obtained assembly with smrt library read […]


Echinochloa crus galli genome analysis provides insight into its adaptation and invasiveness as a weed

PMCID: 5647321
PMID: 29044108
DOI: 10.1038/s41467-017-01067-5

[…] based on the k-mer frequency. the resulting clean reads were assembled into contigs and scaffolds using soapdenovo2 with the default settings. the assembled sequences were further scaffolded with opera-lg v2.0.5, and gaps within the scaffolds were filled using gapcloser v1.1. redundans was used to filter redundant sequences due to heterozygosity. raw pacbio rs long reads were corrected […]


A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication

PMCID: 5628827
PMID: 28981525
DOI: 10.1371/journal.pone.0185310

[…] and a minimum contig size of 200bp was selected. scaffolding with paired-end data was performed as part of the clc de novo assembly. further scaffolding with mate-pair data was performed using opera-lg (v2) []. for opera scaffolding a ploidy level of 1 was specified and mapping of mate-pair reads to contigs was performed with the bwa software package (version 0.7) []., for the gene […]


Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam

PMCID: 5484541
PMID: 28614360
DOI: 10.1371/journal.pntd.0005628

[…] prepare illumina paired-end sequencing libraries with illumina nextera, sequenced on a hiseq2000 to deliver approximately 260x coverage the sequencing reads were then assembled by soapdenovo [] and opera []. genotype-specific dna sequences, which were found in all the genome assemblies of only one genotype, were identified by alignment using nucmer []. blastx analysis of the genotype-specific […]

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Opera institution(s)
NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore

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