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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


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  • person_outline Song Gao <>

Publications for Optimal Paired-End Read Assembler

Opera in pipeline

PMCID: 4833424
PMID: 26975196
DOI: 10.1093/dnares/dsw006

[…] table 1.contigs or scaffolds shorter than 499 bp were excluded., contigs or scaffolds shorter than 499 bp were excluded., for z. matrella ‘wakaba’ and z. pacifica ‘zanpa’, the scaffolds were built by opera using contigs generated by discovar de novo because discovar de novo constructed contigs with higher n50 values than the other assemblers. this may be because only a single mp library was genera […]

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Opera in publications

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 […]

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)., […]

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 […]

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 […]

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 […]

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

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