A simple tool to generate random paired-end FASTQ files for testing and development purposes.

fastqgen creates synthetic paired-end sequencing reads in FASTQ format. The tool generates:

• Random DNA sequences (A, T, C, G)
• Reverse complement mate pairs
• Phred quality scores (Q0-Q40, ASCII 33-73)
• Properly formatted FASTQ output files

Prerequisites:

You need Rust and Cargo installed. If you use conda/mamba:

mamba install -c conda-forge rust
# or
conda install -c conda-forge rust

Alternatively, install Rust from https://rustup.rs

From crates.io

cargo install fastqgen

From Github

cargo install --path .

This will compile the binary and install it to ~/.cargo/bin/ Make sure ~/.cargo/bin is in your PATH.

Basic usage:

fastqgen generate 1000 -l 150 -o my_reads

Arguments:

<N>    Number of reads.

Options:

-o, --outfile <NAME>    Output file prefix [default: synthetic_reads]
-l <LENGTH>             Read length in base pairs [default: 150]
-h, --help              Print help
-V, --version           Print version

The tool generates two files:

<outfile>_R1.fastq      Forward reads
<outfile>_R2.fastq      Reverse reads (reverse complement of R1)

Each FASTQ record contains:

• Header line with read ID and pair indicator (/1 or /2)
• Sequence line
• Plus line separator
• Quality score line

Generate 5000 read pairs of 100bp length:

fastqgen generate 5000 -l 100

MIT

Daniel A. Sprague