FASTQ File Extension

Programs that support FASTQ files

• Windows ⁵
• Mac OS ²
• Linux ²

Windows

• Sublime Text
• PSPad
• Atom
• ChromasPro
• Notepad++

Mac OS

• Atom
• Sublime Text

Linux

• Sublime Text
• Atom

How to open a FASTQ file?

If you cannot open a FASTQ file, it is most often due to missing software. Select a program from the list according to your operating system. Then go to the official website of the program developer, download it, and install it on your device.

Sublime Text, Atom and PSPad stand out as the preferred programs to manage FASTQ files effectively. To install the current version of Sublime Text, go directly to the official Sublime HQ Pty website. The universal package for all operating systems is available there.

After successful installation, your operating system should seamlessly handle FASTQ files via Sublime Text.

Set Sublime Text as the default FASTQ program

Change Default Program on Mac

1. Right click or Control + left click on the desired FASTQ file;
2. Choose "Open in Application" and click "Other";
3. Go to the lower section of the window, where you will find the "Enable" menu. By default, it is set to "Recommended Programs";
4. Select "All Programs" from this menu and proceed to search for Sublime Text. Check the box next to "Always open in app" to set it as the default option.

Set default programs for Windows

1. Start by right-clicking on your FASTQ file, then select the "Open with" option and choose "Choose another app" from the menu that appears;
2. In the pop-up window, select the Sublime Text application;
3. Check the "Always use this application" checkbox, and then click "OK" to apply the selected application as the default for opening FASTQ files.

Convert files to and from FASTQ

For difficult FASTQ files, try converting them to formats like FASTA, SCF or similar formats to improve usability.

Be aware that converting a FASTQ file may reduce some features, but you can usually revert it to the original format.

Convert FASTQ to other file formats

• FASTQ to SCF
• FASTQ to FASTA

Solve problems with FASTQ files

FASTQ files may present some challenges, but most can be easily addressed with minor software tweaks. See the troubleshooting tips below for guidance.

How to edit a FASTQ file?

To make changes to FASTQ files, you need specialized software that allows both opening and editing the data files. Online FASTQ editors offer fewer capabilities than applications optimized for FASTQ format.

Best FASTQ Editor Software in 2026

With the mentioned criteria in mind, we have assembled a selection of FASTQ editors.