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VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Bie M.P. Verbist, Kim Thys, Joke Reumers, Yves Wetzels, Koen Van der Borght, Willem Talloen, Jeroen Aerssens, Lieven Clement, Olivier Thas
2014 Computer applications in the biosciences : CABIOS  
For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations.  ...  Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations.  ...  The authors are grateful to Prof McLachlan and his team for providing the original Fortran code and for giving support to write the R-wrapper.  ... 
doi:10.1093/bioinformatics/btu587 pmid:25178459 fatcat:lgfmoxef3jcz5eaptdmx26ivuu

Recent advances in inferring viral diversity from high-throughput sequencing data

Susana Posada-Cespedes, David Seifert, Niko Beerenwinkel
2017 Virus Research  
Rapidly evolving RNA viruses prevail within a host as a collection of closely related variants, referred to as viral quasispecies.  ...  Advances in high-throughput sequencing (HTS) technologies have facilitated the assessment of the genetic diversity of such virus populations at an unprecedented level of detail.  ...  Acknowledgements We thank Marek Pikulski for his insightful comments and critical reading. Appendix A.  ... 
doi:10.1016/j.virusres.2016.09.016 pmid:27693290 fatcat:mgjzhmio5fhhzpedajjfsskmnu

Bioinformatics Techniques used in Hepatitis C Virus Research

Vikas Kaushik, Bhupender Singh, Joginder Singh
2017 Journal of Pure and Applied Microbiology  
VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering. Bioinformatics 2015;31(1):94-101. Bigger CB, Brasky KM, Lanford RE.  ...  Sequence based in-silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds.  ... 
doi:10.22207/jpam.11.2.32 fatcat:gmukht7wnna2xhkepc5c6dxbca

Technology dictates algorithms: Recent developments in read alignment [article]

Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums (+4 others)
2020 arXiv   pre-print
Aligning reads onto reference genomes enables the identification of individual-specific genetic variants and is an essential step of the majority of genomic analysis pipelines.  ...  Our review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads.  ...  of Illumina reads produced by Influenza A virus quasispecies.  ... 
arXiv:2003.00110v3 fatcat:3l3ad4z5xfhjxoo7snaskartxi

An investigation Into the genetic variation of hepatitis C virus in patients coinfected with HIV

S King
2016
The first focussed on a specific notable polymorphism – Q80K in the NS3 gene – to determine whether deep sequencing would benefit the clinic in the detection of this polymorphism at low frequencies, which  ...  A real-time PCR assay for use with pooled plasma and dried plasma spot specimens was developed to screen a large cohort of HIV-infected individuals from Ghana and assess its suitability for screening in  ...  I am grateful for her support, guidance and patience over the past four years.  ... 
doi:10.17638/02052665 fatcat:pinyz4tiirhqldfryyonzpm4cm

The Evolutionary Potential of Bovine Viral Diarrhea Virus: A Model ssRNA Virus [article]

Adam Alexander Chernick, University Of Calgary, University Of Calgary, Franciscus Johannes Van Der Meer, Karsina Orsel
2016
Methods and results useful for understanding both BVDV and ssRNA viruses in general are presented here. Canadian BVDV isolates were used to infer the evolutionary history of BVDV.  ...  Single stranded RNA viruses are a group of pathogens infecting all animals. They include human pathogens such as human immunodeficiency virus, hepatitis C virus and influenza.  ...  VirVarSeq was used to call both codon-and amino acid-level variants while accounting for nucleotide Q-scores (205) .  ... 
doi:10.11575/prism/28139 fatcat:pymflnifcvgf7btr43hm25uqau