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10.3390/v12070758 http://scihub22266oqcxt.onion/10.3390/v12070758 32674515!7412389!32674515     free     free     free Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Viruses 2020 ; 12 (7): ä Nephropedia Template TP {{tp|p=32674515|t=2020. Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses |pdf=|usr=}}{{32674515}} gab.com Text Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses JO: Viruses http://www.kidney.de/pget.php?&tw=1&pmid=32674515 #FOAvip Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options. Twit Text FOAVip Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses ????Viruses http://www.kidney.de/pget.php?&tw=1&pmid=32674515 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=32674515 #FOAvip English Wikipedia <ref>{{Cite pmid|32674515}}</ref> Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses #MMPMID32674515 Gibson KM; Steiner MC; Rentia U; Bendall ML; Perez-Losada M; Crandall KA Viruses 2020[Jul]; 12 (7): ä PMID32674515show ga Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options. |Betacoronavirus/genetics[MESH] |COVID-19[MESH] |Computational Biology/*methods[MESH] |Coronavirus Infections/virology[MESH] |Genome, Viral[MESH] |Genomics/methods[MESH] |HIV/genetics[MESH] |Haplotypes[MESH] |Hepacivirus/genetics[MESH] |High-Throughput Nucleotide Sequencing/*methods[MESH] |Humans[MESH] |Pandemics[MESH] |Pneumonia, Viral/virology[MESH] |SARS-CoV-2[MESH]Validation of Variant Assembly Using HAPHPIPE with Next-Generation Seq(epmc).pdf DeepDyve Pubget Overpricing