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Opera specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Song Gao

Publications for Optimal Paired-End Read Assembler

Opera citations

 (59)
library_books

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

2018
Extremophiles
PMCID: 5862939
PMID: 29435649
DOI: 10.1007/s00792-018-1011-1

[…] reads 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 in Pyth […]

library_books

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

2018
Genome Announc
PMCID: 5754483
PMID: 29301903
DOI: 10.1128/genomeA.01377-17

[…] ns. 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).Th […]

library_books

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

2017
Front Genet
PMCID: 5723288
PMID: 29259619
DOI: 10.3389/fgene.2017.00180

[…] ding 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 of […]

library_books

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

2017
Nat Commun
PMCID: 5647321
PMID: 29044108
DOI: 10.1038/s41467-017-01067-5

[…] ary 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 by Canu […]

call_split

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

2017
PLoS One
PMCID: 5628827
PMID: 28981525
DOI: 10.1371/journal.pone.0185310
call_split See protocol

[…] sembly 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) []. […]

call_split

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

2017
PLoS Negl Trop Dis
PMCID: 5484541
PMID: 28614360
DOI: 10.1371/journal.pntd.0005628
call_split See protocol

[…] o 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 DN […]

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

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