Influenza Genome Sequencing Application

From a high performance sequencer, 
Automatic distinction of subtypes of influenza viruses
Correspondence of Type A or Type B distinction
Automatically assemble flu viral genome
Available to birds, pigs, horses, humans, and other animals

FluGAS is user-friendly windows software to identify subtypes and distinct a base sequence, as an automatically assembled sequence, for each segment from influenza genome sequence data via a high performance sequencer.

Without a primer sequence selection as a problem of Real Time PCR method, an analysis of either influenza Type A or B is available now. 

  • First software in the world to automatically distinct an influenza subtype directly from Fastq files (recommended in Miseq)

  • A necessary step is just “drag & drop Fastq files” and a batch process with multiple samples is also available

  • Analysis is available without setting of a primer sequence

  • Correspondence to both influenza type A and type B

  • In case of influenza type A, this software identifies up to the subtype (HA, NA) whereas in case of influenza type B, the existence of viruses in samples will be clarified

  • A consensus sequence of all eight segments will be automatically created

  • Reference database to identify a subtype is registered sequences from NCBI Influenza virus resource

  • Easy management of results: a result includes both an excel file in GISAID format and a PDF file for each sample, and the result of multiple samples will be also exported as a tab separated text file

  • An analysis result will be saved in the application, and by selecting a time period of analysis, results in the time frame can be exported together

  • Database can be automatically updated

The difference of type A and type B flu viruses:

Type A flu infects various animals including humans through birds as natural hosts.

Type B flu is found only in humans, and there are few reports that it infected other animals. Some studies show sea lions carry flu viruses via humans.

Automatic Analysis Process

Enter Fastq Files

Sequence data verified by this software is a Fastq file from Illumina MiSeq

QC check

Quality Control of read data (Trimming based on Phread score and read length)


Multiple times of mapping to prepared reference sequences for each segment
(automatic genome assembly)

Determine subtypes

Create a consensus sequence from the mapping result and determine a subtype.

*In case of type B flu, the subtype determination will not be performed but the examination of the type B, and its consensus sequence with 8 segments will be exported.


The result will be exported in both an excel file in GISAID format and PDF file.
System requirement:
OS: Windows 7 or later
Memory:16Gbyte or more
Hard Disk Capacity: recommended 200Gbyte~1T 
CPU: recommended Intel Core i7 or more

Development collaborator:

National Institute of Animal Health, National Agriculture and Food Research Organization

For more details, please contact us.