<?xml version="1.0" encoding="utf-8" standalone="yes"?><feed xmlns="http://www.w3.org/2005/Atom"><generator uri="https://gohugo.io" version="0.141.0">Hugo v0.141.0</generator><id>https://millironx.millironx.page/@indiewebpub/tags/quasispecies/</id><link rel="self" type="application/atom+xml" href="https://millironx.millironx.page/@indiewebpub/tags/quasispecies/feed.xml"/><link rel="alternate" type="text/html" href="https://millironx.millironx.page/@indiewebpub/tags/quasispecies/"/><updated>2025-03-31T00:14:19+00:00</updated><title>All content tagged "quasispecies" on Milliron X</title><entry><id>https://millironx.millironx.page/@indiewebpub/academia/yavsap/</id><link rel="alternate" href="/academia/yavsap/yavsap.pdf"/><title>YAVSAP: versatile viral quasispecies analysis for veterinary samples</title><published>2024-03-05T00:00:00+00:00</published><updated>2024-03-05T00:00:00+00:00</updated><author><name>Thomas A. Christensen II</name><uri>https://millironx.millironx.page/@indiewebpub/people/thomas-a.-christensen-ii/</uri></author><author><name>Steven Stancic</name><uri>https://millironx.millironx.page/@indiewebpub/people/steven-stancic/</uri></author><author><name>Andrea Lu</name><uri>https://millironx.millironx.page/@indiewebpub/people/andrea-lu/</uri></author><author><name>Dana Mitzel</name><uri>https://millironx.millironx.page/@indiewebpub/people/dana-mitzel/</uri></author><author><name>William Wilson</name><uri>https://millironx.millironx.page/@indiewebpub/people/william-wilson/</uri></author><author><name>Rachel Palinski</name><uri>https://millironx.millironx.page/@indiewebpub/people/rachel-palinski/</uri></author><category term="presentation"/><category term="virus"/><category term="quasispecies"/><category term="next-generation sequencing"/><category term="pipeline"/><summary type="text">
Viral populations within an infected host are composed of viral particles with a spectrum of genetic mutations rather than a unified genome. This phenomenon is referred to as viral “quasispecies,” and has been useful for the understanding of viral transmission and early detection of new viral variants. Next generation sequencing (NGS) has enabled the study of these quasispecies for many viral species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV2), and established protocols and computer analysis tools have been developed for these species. Some of the most important viruses, such as emerging and exotic disease agents, however, do not have replicatable protocols or software tools capable of producing valid output from their sequence data. Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP is a fully automated bioinformatic pipeline built from the ground up to identify and analyze viral quasispecies of any arbitrary virus in human and veterinary samples. YAVSAP provides reference-based genome mapping of both long- and short-read sequencing reads to any reference genome that the user chooses, identifies subconsensus variants and haplotypes, and assesses the phylogenies of all viral sequences found within a sample. YAVSAP is written in Nextflow and conforms to the nf-core initiative’s standards, which allows it to run on low-end computers, high performance computing (HPC) clusters, or anything in between with zero configuration. YAVSAP has been tested on viruses of interest to veterinary medicine and public health, including Japanese Encephalitis Virus (JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift Valley Fever Virus (RVFV), and can correctly identify consensus genomes and quasispecies within samples containing each of these viruses. This tool provides a means for biologists with little bioinformatic experience to analyze deep sequence data while correcting for many of the pitfalls associated with previous and current analysis platforms. YAVSAP is open source software and is publicly available at https://github.com/ksumngs/yavsap.</summary><content type="html" xml:lang="en" xml:base="https://millironx.millironx.page/@indiewebpub/">
&lt;p>Viral populations within an infected host are composed of viral particles with a
spectrum of genetic mutations rather than a unified genome. This phenomenon is
referred to as viral &amp;ldquo;quasispecies,&amp;rdquo; and has been useful for the understanding
of viral transmission and early detection of new viral variants. Next generation
sequencing (NGS) has enabled the study of these quasispecies for many viral
species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and
Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2
(SARS CoV2), and established protocols and computer analysis tools have been
developed for these species. Some of the most important viruses, such as
emerging and exotic disease agents, however, do not have replicatable protocols
or software tools capable of producing valid output from their sequence data.
Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP
is a fully automated bioinformatic pipeline built from the ground up to identify
and analyze viral quasispecies of any arbitrary virus in human and veterinary
samples. YAVSAP provides reference-based genome mapping of both long- and
short-read sequencing reads to any reference genome that the user chooses,
identifies subconsensus variants and haplotypes, and assesses the phylogenies of
all viral sequences found within a sample. YAVSAP is written in Nextflow and
conforms to the nf-core initiative&amp;rsquo;s standards, which allows it to run on
low-end computers, high performance computing (HPC) clusters, or anything in
between with zero configuration. YAVSAP has been tested on viruses of interest
to veterinary medicine and public health, including Japanese Encephalitis Virus
(JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift
Valley Fever Virus (RVFV), and can correctly identify consensus genomes and
quasispecies within samples containing each of these viruses. This tool provides
a means for biologists with little bioinformatic experience to analyze deep
sequence data while correcting for many of the pitfalls associated with previous
and current analysis platforms. YAVSAP is open source software and is publicly
available at &lt;a
 href="https://github.com/ksumngs/yavsap">https://github.com/ksumngs/yavsap&lt;/a>.&lt;/p>
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