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SOPRA specifications

Information


Unique identifier OMICS_00049
Name SOPRA
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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Publication for SOPRA

SOPRA citations

 (13)
library_books

A Possible Trifunctional β Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105

2018
Genes
PMCID: 5924542
PMID: 29642531
DOI: 10.3390/genes9040200

[…] eads (Illumina, San Diego, CA, USA) were combined and assembled de novo using GS De Novo Assembler version 2.6 (Newbler, Roche, Basel, Switzerland) []. Then, subsequent scaffolding was performed with SOPRA [] and SSPACE [] using Illumina mate-pair information. At least five consistent read-pairs were needed to form a connection. Gaps inside scaffolds were closed with Illumina paired-end data using […]

library_books

Draft Genome Sequence of the Oleaginous Green Alga Tetradesmus obliquus UTEX 393

2017
Genome Announc
PMCID: 5255914
PMID: 28104651
DOI: 10.1128/genomeA.01449-16

[…] ing, and the resulting scaffold sets were merged. In the first method, contigs were assembled using IDBA-UD version 1.1.1 (), producing a 96,197,736-bp assembly in 9,191 contigs, and scaffolded using SOPRA version 1.4.6 (), as previously recommended (), to obtain 2,509 scaffolds. In the second method, contigs were assembled using CLC Genomics Workbench version 5.1, producing a 93,347,907-bp assemb […]

library_books

Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae

2017
Sci Rep
PMCID: 5238449
PMID: 28091569
DOI: 10.1038/srep40655

[…] rst filtered by removing all sequences mapping to the Anopheles gambiae genome version AgamP4 (https://www.vectorbase.org/). Remaining reads were assembled into contigs and scaffolds using Velvet and SOPRA. Filtered reads uniquely mapped to the P. falciparum reference genome were merged with assembled scaffolds to get all reference genomic regions matching sequences present in the Burkina dataset. […]

library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] MEM for read alignment (). The source code of the ABySS package is available at the address http://www.bcgsc.ca/platform/bioinfo/software/abyss, and is developed to work on the Linux operating system.SOPRA (): This scaffolding tool was designed to improve assemblies generated by Velvet () and SSAKE (), and targets the earlier sequencing platforms from Illumina and ABI SOLiD. The program parses the […]

library_books

Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment

2016
Mol Biol Evol
PMCID: 5854124
PMID: 28007977
DOI: 10.1093/molbev/msw230

[…] led the genomes using ALLPATH-LG (). To increase scaffold length, reads from mate-pairs of different insert sizes were added step-by-step for scaffolding using SSPACE (), SOAPdenovo (), Opera (), and SOPRA (). Finally, we used the paired-end information from the short paired-end reads to fill the gaps between the scaffolds with Gapcloser in SOAPdenovo and Gapfiller ().We used three approaches for […]

library_books

Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation

2016
PLoS One
PMCID: 4976891
PMID: 27500531
DOI: 10.1371/journal.pone.0160336

[…] for re-scaffolding the ALLPATHS-LG assembly. The genome scaffold L50 was improved to 296,016 bp. Next, ICORN2 [] was used to correct SNPs and InDels, and GapFiller [] was used to close gaps. Finally, SOPRA [] was used for re-scaffolding again, and ICORN2 and GapFiller were used in turn to obtain the final genome assembly. […]

Citations

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SOPRA institution(s)
Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, USA

SOPRA review

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Has not been updated since 2011, appears to be no longer in active development.