fastq read simulator
This software is dual-licensed:
- Open-source under the GNU GPL v3 for academic and non-commercial use
- Commercial license required for proprietary, industrial, or SaaS usage
For commercial licensing, contact: Alar.Aints@gmail.com
ReadGen © Alar Aints 2026 a program for generating simulated fastq sequence reads
Options:
-l Read Length [100]
-n number of reads to generate [1000000]
-m mutation probability % per base [0]
-o outfiles (optional)
-p paired output, no argument. Single by default
-O where the outfiles go (Optional. By default the outfiles go to the same folder as input files.)
-t title tag for title lines (optional)
-L readlimit. 0 reads the whole files [0]
-i input file(s). Many files can be entered, gap separated. Fasta format only
-F only forward reads output
-R only reverse reads output
-B output reads both ways mixed
System requirements
Disk space: using default settings, one outfile with 1M reads of 100 bp takes about 250 MB.
Memory: Largest infile size + 1 MB
Dependencies: ReadGen has no dependencies. ReadGen is written in C.
File formats: Input: fasta format only. Output: fastq format. Single or paired reads can be generated, -F forward, -R reverse, -B mixed orientation.
MacOS notice: ReadGen runs on MacOS and Linux.
Network connectivity: ReadGen has no network connectivity functions. All files must be available locally.
Multihreading: ReadGen runs on a single thread
Behaviour Input files: -i FOLDER/. can be used. Only fasta files will be processed. Output files: -o none, one or two files can be specified. Outfile names will be completed automatically. Outfiles are written in fastq format. If -p is set, two output files with paired reads will be generated. If -t is specified, read names will contain this title tag. If not specifed, title tag is derived from filename. Output path -O can be specified, outfiles will be written in this folder. If the folder does not exist, it will be created. Number of reads -n applies per infile. Readlimit -L applies per infile. Output from successive infiles will be appended to the outfiles.