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Identify the COVID-19 genome sequence and its variant from a sequencer

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Compatible with sequencers from Illumina MiSeq and Oxford Nanopore

All analysis is completed on Windows

CovGAS： Automatic Corona virus Genome Assembly Software

It has been verified that analysis of Omicron strains can also be performed by automatic database update. No particularly difficult operations are required.

CoVGAS uses an algorithm that is strong in detecting mutant strains.
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Through a workflow designed for COVID-19, data from a sequencer will be automatically processed, including the following steps.

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  • 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.

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  • 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.
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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.
CoVGAS Video

CoVGAS Video

Play Video

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）

License

Perpetual / PC

CoVGAS (COVID-19) genome sequence analysis software is easy to use for an analysis of “COVID-19” sequence data, exported from a next generation sequencer to evaluate genome sequence analysis on a 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）
 

  • Program file

  • Manual to set up

  • Manual

  • Database 

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.
covgastrial
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