Opera protocols

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 pipelines

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

[…] 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 […]

PMCID: 4446112
PMID: 25887666
DOI: 10.1186/s12864-015-1498-0

[…] finally, the plastome assembly with k-mer = 65 was used for all subsequent analyses in both species. the selected velvet assembly was further scaffolded using optical read mapping as implemented in opera [75]. assembled scaffolds were further error corrected using the sequel software by re-mapping the reads and extending/correcting the ends of the scaffolded regions [76]. gap filling […]

PMCID: 3990754
PMID: 24744338
DOI: 10.1128/genomeA.00320-14

[…] picotiter plates. the 454 sequencing generated 362,293 reads assembled into contigs and scaffolds using newbler version 2.8 (roche, 454 life sciences). contigs obtained were combined together using opera software v1.2 (11) and gapfiller v1.10 (12) to reduce the set. finally, some manual refinements using clc genomics v5 software (clc bio, aarhus, denmark) improved the genome. the draft genome […]

PMCID: 4149013
PMID: 25197492
DOI: 10.4056/sigs.5501035

[…] 70×75 and sequenced with the gs flx titanium sequencing kit xlr70., the 454 sequencing generated 650,718 reads (104,82 mb) assembled into contigs and scaffolds using newbler version 2.8 (roche) and opera software v1.2 [37] combined with gapfiller v1.10 [38] and some finishing using clc genomics workbench. finally, the available genome consists of 8 scaffolds and 26 contigs, with a 43.71× […]

PMCID: 3910703
PMID: 24501638
DOI: 10.4056/sigs.4177252

[…] filter sequences generated 71.95mb with a length average of 325bp., the 454 sequencing generated 607,067 reads (105,03 mb) assembled into contigs and scaffolds using newbler version 2.7 (roche) and opera software v1.2 [42] combined to gapfiller v1.10 [43]. finally, the available genome consists of 14 scaffolds and 53 contigs, with a coverage of 44.9., non-coding genes and miscellaneous features […]

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

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