A Java-based FASTQ file generator for bioinformatics testing and development.

FastqGen is a lightweight tool that generates simulated FASTQ files with random DNA sequences. FASTQ files are text-based format for storing both biological sequence data (usually nucleotide sequence) and its corresponding quality scores. This tool is particularly useful for:

• Testing bioinformatics pipelines
• Benchmarking sequence analysis tools
• Development and debugging of NGS data processing applications
• Educational purposes in bioinformatics

• Generates valid FASTQ format files
• Command-line configurable sequence length and file size
• Random DNA sequence generation using standard nucleotides (A, T, C, G)
• Phred quality score simulation
• Automatic timestamp-based file naming

The program requires two command-line arguments:

java -jar fastqgen.jar <sequenceLength> <fileSizeInMB>

Parameters:

• sequenceLength: Length of each DNA sequence in base pairs (e.g., 100)
• fileSizeInMB: Desired output file size in megabytes (e.g., 10)

Example:

java -jar fastqgen.jar 150 20    # Generates sequences of 150bp with a total file size of 20MB

The output filename is automatically generated with format: simulated_YYYYMMDDHHMMSS.fastq

Each entry in the generated FASTQ file consists of four lines:

1. Sequence identifier (starts with '@')
2. Raw sequence letters
3. Separator line (starts with '+')
4. Quality scores (encoded in ASCII)

Example:

@SEQ1
ATCGATCG...
+
IIIIIII...

• Java JDK 8 or higher
• Maven (for building)

mvn clean package

After building, you can run the application using the generated jar in the target directory:

java -jar fastqgen.jar <sequenceLength> <fileSizeInMB>

Example:

java -jar fastqgen.jar 100 10    # Generates 100bp sequences in a 10MB file

• Quality scores are generated using Phred-like quality values
• Sequences are randomly generated using equal probabilities for A, T, C, G
• Each generated file includes a unique timestamp in its name for easy identification

MIT License

Contributions are welcome! Please feel free to submit a Pull Request.