Readme
FASTQGEN
A simple tool to generate random paired-end FASTQ files for testing and
development purposes.
DESCRIPTION
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
INSTALLATION
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.
USAGE
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
OUTPUT
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
EXAMPLES
Generate 5000 read pairs of 100bp length:
fastqgen generate 5000 - l 100
LICENSE
MIT
AUTHOR
Daniel A. Sprague