About: COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM

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About: COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM
Creator	Gascuel, Olivier Blassel, Luc Lemoine, Frédéric Voznica, Jakub
Source	BioRxiv
abstract	Motivation The first cases of the COVID-19 pandemic emerged in December 2019. Until the end of February 2020, the number of available genomes was below 1,000, and their multiple alignment was easily achieved using standard approaches. Subsequently, the availability of genomes has grown dramatically. Moreover, some genomes are of low quality with sequencing/assembly errors, making accurate re-alignment of all genomes nearly impossible on a daily basis. A more efficient, yet accurate approach was clearly required to pursue all subsequent bioinformatics analyses of this crucial data. Results hCoV-19 genomes are highly conserved, with very few indels and no recombination. This makes the profile HMM approach particularly well suited to align new genomes, add them to an existing alignment and filter problematic ones. Using a core of ∼2,500 high quality genomes, we estimated a profile using HMMER, and implemented this profile in COVID-Align, a user-friendly interface to be used online or as standalone via Docker. The alignment of 1,000 genomes requires less than 20mn on our cluster. Moreover, COVID-Align provides summary statistics, which can be used to determine the sequencing quality and evolutionary novelty of input genomes (e.g. number of new mutations and indels). Availability https://covalign.pasteur.cloud, hub.docker.com/r/evolbioinfo/covid-align Contacts olivier.gascuel@pasteur.fr, frederic.lemoine@pasteur.fr Supplementary information Supplementary information is available at Bioinformatics online.
has issue date	2020-05-25(xsd:dateTime)
bibo:doi	10.1101/2020.05.25.114884
has license	biorxiv
sha1sum (hex)	d9461d15391d6a3dcfc64446d5841c15e2818fb6
schema:url	https://doi.org/10.1101/2020.05.25.114884
resource representing a document's title	COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM
schema:publication	bioRxiv
resource representing a document's body	covid:d9461d15391d6a3dcfc64446d5841c15e2818fb6#body_text
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