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ViSpA specifications

Information


Unique identifier OMICS_05853
Name ViSpA
Alternative name Viral Spectrum Assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux
Programming languages Java, Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Additional information


https://sourceforge.net/projects/viralspectrumas/?source=navbar

Publication for Viral Spectrum Assembler

ViSpA citations

 (6)
library_books

Effect of adding nanometre sized heterogeneities on the structural dynamics and the excess wing of a molecular glass former

2016
Sci Rep
PMCID: 5057163
PMID: 27725747
DOI: 10.1038/srep35034

[…] nt NSE technique evidently is mainly sensitive to the α-relaxation mode (cf. diamonds in ). It should be noted that the obtained relaxation-time values at 〈Q〉 = 1.3 Å−1 and 1.5 Å−1 are quite similar. Vispa et al. [ref. ] have shown that at Q = 1.3 Å−1 the data for incoherent NS matches with the DS data where the coherent contribution is negligible. The combination of our BS and NSE studies points […]

library_books

Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness

2015
BMC Bioinformatics
PMCID: 4682401
PMID: 26678073
DOI: 10.1186/1471-2105-16-S18-S3

[…] A number of unsupervised Quasispecies Spectrum Reconstruction (QSR) methods such as ShoRAH [], QuRe [], PredictHaplo [], ViSpA [] and QuasiRecomb [] are available in literature. Comprehensive reviews on these methods are presented in [] and []. We recently formulated a novel unsupervised method named ViQuaS [] for QSR a […]

library_books

Viral quasispecies inference from 454 pyrosequencing

2013
BMC Bioinformatics
PMCID: 4234478
PMID: 24308284
DOI: 10.1186/1471-2105-14-355

[…] ively a copy of one of the previous (i – 1) variants except at the mutation sites. The resultant genome sequences thus constitute the true data that we will attempt to reconstruct with QuasQ, ShoRAH, ViSpA, QuRe and QuasiRecomb. Aside from varying the total number of sequences generated, we vary, too, the frequencies of each of these sequences and finally used ART 454 to generate reads of differen […]

library_books

Reconstruction of viral population structure from next generation sequencing data using multicommodity flows

2013
BMC Bioinformatics
PMCID: 3698000
PMID: 23902469
DOI: 10.1186/1471-2105-14-S9-S2

[…] reasing quality of the solution. Moreover, instead of increasing the size of the network, AmpMCF allows to decrease it, thus making the problem much more computationally tractable.ShotMCF extends the ViSpA algorithm described in []. The method proposed in [] consists of two stages: generation of candidate quasispecies sequences from shotgun NGS reads using Maximum Bandwidth paths in the read graph […]

library_books

Challenges and opportunities in estimating viral genetic diversity from next generation sequencing data

2012
Front Microbiol
PMCID: 3438994
PMID: 22973268
DOI: 10.3389/fmicb.2012.00329

[…] s the search for a set of haplotypes covering all reads with minimum costs (Westbrooks et al., ) and, in a slightly different fashion relaxing the requirement of a complete read cover, implemented in ViSpA (Astrovskaya et al., ). The combinatorial reconstruction is followed by frequency estimation using an Expectation Maximization (EM) algorithm (Eriksson et al., ; Westbrooks et al., ; Astrovskaya […]

library_books

Haplotype and minimum chimerism consensus determination using short sequence data

2012
BMC Genomics
PMCID: 3394418
PMID: 22537299
DOI: 10.1186/1471-2164-13-S2-S4

[…] to thank Prof. Jessica Hellmann for bringing this problem to our attention and members of the Hellmann lab for data preparation and useful discussions. We also thank Irina Astrovskaya for sharing the ViSpA manuscript preprint. This work was supported in part by a fellowship to STO as part of the University of Notre Dame's strategic research investment in global health.This article has been publish […]

Citations

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ViSpA institution(s)
Department of Computer Science, Georgia State University, Atlanta, GA, USA

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