Viral Spectrum Assembler

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]