Windows
Compatible applications
Quick Facts
Basic information about this file format
Extension
.FASTQ
File Type
FASTQ format
Category
Data
Best first step
Use compatible software
Quick Summary
A practical overview of the .fastq file format
The FASTQ format is a text-based file format used for storing biological sequence data, specifically the output from high-throughput DNA sequencing instruments. It is the de facto standard for storing both the raw nucleotide sequence and its corresponding quality scores. A FASTQ file typically uses…
File extension
.FASTQ
File type
FASTQ format
Category
Data
Recommended action
Open with a trusted compatible app
How to open a .fastq file
Start with a trusted app that supports this format
- Check the file extension carefully and confirm that the file name really ends with .fastq.
- Use software that supports this file type. If one app does not work, try another compatible program for the same platform.
- Update the application if the file was created by a newer version of the software.
- Scan files from unknown sources before opening them, especially documents, archives, scripts, installers, and executable files.
What is a .fastq file?
File extension details and usage information
The FASTQ format is a text-based file format used for storing biological sequence data, specifically the output from high-throughput DNA sequencing instruments. It is the de facto standard for storing both the raw nucleotide sequence and its corresponding quality scores. A FASTQ file typically uses four lines per sequence: the first line begins with an '@' character followed by a sequence identifier and optional description; the second line contains the raw sequence letters; the third line begins with a '+' character and is optionally followed by the same sequence identifier; and the fourth line encodes the quality values for the sequence in the second line, using ASCII characters to represent numerical quality scores. These quality scores are critical for downstream bioinformatics analysis, as they allow researchers to assess the reliability of each base call, which is essential for variant calling, genome assembly, and transcriptomics. Because of the massive volume of data generated by modern sequencers, FASTQ files are frequently compressed using gzip, resulting in the common .fastq.gz extension.
Software Compatibility
Programs that may open or work with .fastq files
macOS
Compatible applications
Linux
Compatible applications
Mobile
Mobile applications
Can .fastq files be converted?
Options for saving or exporting this file to another format
In many cases, a .fastq file can be converted by opening it in compatible software and using an option such as Save As, Export, or Convert. The available output formats depend on the file type and the application used.
- Use the original software that created the file when possible.
- Check whether the application supports exporting to common formats.
- Be careful with online converters when working with private, business, or sensitive files.
- If conversion fails, the file may be corrupted, incomplete, encrypted, or not actually a .fastq file.
Why can't I open a .fastq file?
Common reasons this file type may not open correctly
Wrong software
The file may require a specific program that supports the .fastq format.
Incorrect extension
The file extension may have been renamed manually, even though the actual file format is different.
Corrupted file
The file may be incomplete, damaged during download, or transferred incorrectly.
Outdated app
Your software may need to be updated before it can open newer versions of this file format.
Frequently Asked Questions
Common questions about .fastq files
To open a .fastq file, use software that supports this file format.
- Notepad++
- CLC Genomics Workbench
- Geneious Prime
- TextEdit
- IGV (Integrative Genomics Viewer)
Open the file in compatible software and look for options such as Save As, Export, or Convert. If no export option is available, the file may require a specialized converter or the original application that created it.
- Verify that the file extension is correct.
- Install or update compatible software.
- Try another application that supports this format.
- Check whether the file is corrupted, incomplete, or encrypted.
A file extension alone does not guarantee whether a file is safe or unsafe. Only open files from trusted sources, scan unknown files before opening them, and be especially careful with executable, script, archive, and document files.
File safety tips
Use caution with unknown files
Only open files from trusted sources. Before opening a .fastq file, scan it with antivirus software, verify that the file extension is expected, and avoid running unknown executable, installer, macro-enabled document, or script files.