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Automatic distinction of HA and NA subtypes of influenza virus from a sequencer

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Compatible with sequencers from Illumina MiSeq and Oxford Nanopore

All analysis is completed on Windows

FluGAS: Automatic Influenza Genome Assembly and Subtyping

Through a workflow designed for COVID-19, data from a sequencer will be automatically processed, including the following steps.

  • Identification of a genome sequence

  • Extraction of amino acid variations against a reference sequence

  • Identification of a Nextclade type or Pangolin type

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* A reference sequence, used to detect variants, is used from NC_045512(Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1).

*A genome sequence will be created based on a mapping result from an optimal virus strain (as a reference sequence), registered as COVID-19 reference database in NCBI Virus.

  • CoVGAS shows an identification of similar strains, clade information, and information of closely related strains as a result of a genome sequence analysis.
  • Also, CoVGAS provides information of a genome sequence from a sample, the accompanying information of the NCBI Virus Database registered COVID-19 strain which has the highest homology with the sequence, and information of a collected location and date.
Result of COVID-19 from a sample, including variants, closely related strains (collected location and date) and a variant type.

Compatible with sequencers from Illumina MiSeq and Oxford Nanopore

All analysis is completed on Windows

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  • All processes in GoVGAS will be performed on the Windows PC, an analysis will start by drag-and-drop sequence data, and the result will be automatically displayed.
  • There are no command lines or difficult procedures. Any organizations that use sequencers can utilize CoVGAS.
  • Data from Illumina MiSeq or Oxford Nanopore can be easily switched.
*If an exported Fast5 file from a Nanopore sequencer without a basecall is used or a barcode segmentation is necessary for each sample, the Guppy windows version needs to be used. 
Function list
  • Compatible with Fastq files (Illumina/Oxford Nanopore sequencer)

  • By drag-and-drop sample files to the CovGAS app, automatically identifications of genome sequences and types will be processed

  • The genome sequence will be displayed on the app window and exported as a Fasta file

  • Information of consensus sequences along with NCBI registered closely related strains (collected location, date, and Genbank Accession)

  • Reference cover rate and average coverage from a mapping result of the final consensus and the similar strain.

  • From a mapping result of COVID-19, variant information in a VCF format and conversion to amino acid variants

  • Connection to Aliment Viewer (AliView) and Mapping Viewer (Tablet)

  • Removal of a Primer sequence of Illumina Pairend sequence (Alt-nCov2019_primers)

  • Identification of a Nextclade typerom sample variants (need to enter an exported consensus sequence to the Nextclade site)

  •  Identification of a Pangolin type from a consensus sequence (Pangolin lineage)

  • Automatically update the latest similar strain sequence database

*Installing Guppy, provided by Nanopore, CoVGAS will be compatible with samples in a Fast5 raw-data format.
FluGAS (Influenza virus) genome sequence analysis and automatic distinction of HA and NA subtypes of influenza virus software is easy to use for an analysis of “Influenza virus” sequence data, exported from a sequencer to evaluate genome sequence analysis on a Windows GUI. 
Analysis workflow
1. Sequence data
  • Drag-and-drop a Fastq (or multiple files)

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An image of entering sequence data. Select either MiSeq or MinION and drag-and-drop sequence data.

2. QC check (self-executing)
  • Quality Control of read data (trimming based on Phread score the read length)

3. Mapping (self-executing)
  • Mapping the Fastq file, which passed the QC, to a reference sequence, retrieved from NCBI.

  • There are two mappings; creating a consensus sequence after the 1st mapping and executing the 2nd mapping based on this consensus sequence. Contact us for more details of this algorithm. 

4. Identification of a ge nome sequence and similar strains (self-executing)
  • Based on the mapping method, similar strains from NCBI will be listed. 

3. Mapping (self-executing)
  • This example shows that MW084426.1 is the closest strain, registered in NCBI. 

  • From MW084426.1, information, such as the date of sample collection, the collected location, etc can be obtained. 

  • This example identifies as a GH type, described as GISAID, and it shows that 5 of variant locations out of 7 in the Nextclade 20H (Beta, V2) variant are common and assigned Pangolin Lineage B.1.2. 

  • From a mapping result, using MW084426.1 as a reference, the average coverage, the cover ration, and the consensus sequence are displayed. 

  • From the character strings of Nextclade and Pangolin, a browder will start. By entering the displayed consensus sequence, details can be obtained for each site. 

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Trial

We provide a 2-weeks trial of this program. 

Fill out the form, then we will send download link. 

Ver 1.0 Setup fiile

 CovGAS.zip (1.6GB)‐2021/7/19
 

  • Program file

  • Manual to set up

  • Manual

  • Database (2021/7/10)

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Specification

CPU:Core i5/ i7 or higher(8th generation or higher is recommended)

Memory:8Gb(16Gb or higher is recommended)

Storage: 1Tb or higher is recommended(Install storage 500Gb)

O  S   : Windows 10 64bit (version 1709 or later)

! After installing, the latest database will be automatically uploaded. Please install this program while connecting to the Internet.