SOPRA protocols

View SOPRA computational protocol

SOPRA statistics

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Associated diseases

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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 in pipeline

2014
PMCID: 4110763
PMID: 25013135
DOI: 10.1128/genomeA.00617-14

[…] sequencing was performed using the illumina miseq, according to the manufacturer’s protocols, to generate 2 × 150 bp reads, which were assembled using spades version 3.0 and scaffolded using sopra version 1.4.6 to give an assembly size of 3.98 mb, with an n50 of 363 kb (, ). the gene predictions and annotations were performed using the computational genomics pipeline (cg-pipeline) […]


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SOPRA in publications

 (60)
PMCID: 5897367
PMID: 29650968
DOI: 10.1038/s41598-018-23221-9

[…] a ge diode detector and a si/caf2 beam splitter. in addition, the optical properties in the spectral range from 1.24 ev to 5.45 ev were investigated by means of spectroscopic ellipsometry using a sopra ges5e ellipsometer and an angle of incidence of 75°. the ellipsometry data served as an additional reference for the fitting of the ftir data, which is the main focus of the current paper. […]

PMCID: 5924542
PMID: 29642531
DOI: 10.3390/genes9040200

[…] (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 […]

PMCID: 5862832
PMID: 29563557
DOI: 10.1038/s41598-018-23360-z

[…] spot was observed using an atomic force microscope (veeco multimode v). the optical constant of the ge2sb2te2 thin film at different optical states was measured using a spectral ellipsometer (sopra ges5e uv/vis/ir). crystal structure analysis for the as-deposited films and laser-irradiated spots was carried out by micro-area x-ray diffraction (rigaku d/max-2550)., publisher's note: […]

PMCID: 5816388
PMID: 29454370
DOI: 10.1186/s12985-018-0949-z

[…] non-identified bats of the genus pipistrellus., the case concerns an adult female of pipistrellus kuhlii, who was found to be spontaneously dead in a wildlife recovery center in valpredina, cenate sopra (bg), northern italy. the sick bat was originally found alive on september 29th, 2016 in vaprio d’adda village (bergamo province, northern italy) by a private citizen who brought […]

PMCID: 5760491
PMID: 29318402
DOI: 10.1186/s11671-017-2414-0

[…] (xrd) (bruker d8 discover), atomic force microscopy (afm) (bruker icon), x-ray photoelectron spectroscopy (xps) (kratos axis ultra dld), ultraviolet-visible spectroscopy (uv-vis), and ellipsometer (sopra ges-se, france), respectively. the electrical measurements of the devices were performed using a semiconductor parameter analyzer (b1500a, agilent technologies, japan) with cascade probe […]


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

SOPRA review

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Michael Gribskov

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