- #Clc sequence viewer reference update
- #Clc sequence viewer reference software
- #Clc sequence viewer reference free
The rate of virus evolution is further shaped by the impact of the mutations on the viral fitness as well as by host immunity-related factors or ecological and environmental mechanisms, which ultimately drive the timing and frequency of the emergence of novel epidemic threats. New viral variants emerge constantly due to the never-ending viral genetic and antigenic modification as a consequence of mutation events such as the misincorporation of nucleotides during genome replication or the exchange of genomic segments. Influenza virus represents a major public health concern worldwide as it causes annual seasonal epidemics and occasional pandemics leading to high morbidity and mortality in the population. In summary, INSaFLU supplies public health laboratories and influenza researchers with an open “one size fits all” framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. This platform additionally flags samples as “putative mixed infections” if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional “consensus-based” influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. Data integration is thus cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics.
#Clc sequence viewer reference update
INSaFLU gives access to user-restricted sample databases and projects management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded.
#Clc sequence viewer reference software
By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform multi-step software intensive analyses in a user-friendly manner without previous advanced training in bioinformatics.
#Clc sequence viewer reference free
We developed and implemented INSaFLU (“INSide the FLU”), which is the first influenza-oriented bioinformatics free web-based suite that deals with primary NGS data (reads) towards the automatic generation of the output data that are actually the core first-line “genetic requests” for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants’ annotation, alignments and phylogenetic trees). Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale.
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