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123Fastq download for Windows

Free download 123Fastq Windows app to run online win Wine in Ubuntu online, Fedora online or Debian online

This is the Windows app named 123Fastq whose latest release can be downloaded as 123Fastq_v1.3.rar. It can be run online in the free hosting provider OnWorks for workstations.

Download and run online this app named 123Fastq with OnWorks for free.

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- 6. Download the application and install it.

- 7. Download Wine from your Linux distributions software repositories. Once installed, you can then double-click the app to run them with Wine. You can also try PlayOnLinux, a fancy interface over Wine that will help you install popular Windows programs and games.

Wine is a way to run Windows software on Linux, but with no Windows required. Wine is an open-source Windows compatibility layer that can run Windows programs directly on any Linux desktop. Essentially, Wine is trying to re-implement enough of Windows from scratch so that it can run all those Windows applications without actually needing Windows.





123Fastq, as the first member of 123NGS family, performs all the pre-processes around next-generation sequencing reads (FASTQ files) easier than ever in the field of open source tools. 

Download quick user manual for the latest version:

This work has been done under the supervision of
Dr.Javad Zahiri,
Department of Neurosciences, University of California San Diego,
Bioinformatics and Computational Omics Lab (BioCOOL)


Dr.Masoud Garshasbi,
Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.


  • Next generation sequencing reads quality check
  • Quality check of paired-end reads
  • Flexible trimmer
  • Trim recommendations based on quality check results
  • Adapter decontamination by two approaches
  • Fast5 to FASTQ conversion
  • SAM/BAM to FASTQ conversion
  • Cross platform (unix, windows)
  • Written in java

User interface

Java Swing

Programming Language


This is an application that can also be fetched from https://sourceforge.net/projects/project-123ngs/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.