MaSTRspy is a GUI-based pipeline for forensic STR profiling from nanopore and long-read sequencing data. It accepts raw sequencing output (POD5, BAM, or FASTQ), filters reads for quality, aligns them to a 45-locus STR reference database (GRCh38), and produces per-sample allele calls, STR profiles, and plots.
Compatibility: Verified on Linux and macOS.
git clone https://github.com/DP-Genome/MaSTRspy.git
cd MaSTRspy
conda env create -f environment.yml
conda activate mastrspy
mastrspy setupThe setup command auto-detects all installed tools and writes their paths to config/ToolsConfig.txt.
Run mastrspy setup again after installing Dorado or xatlas to activate those features.
Launch the GUI:
mastrspy activateThe wizard guides you through the following steps:
- File Selection — point to your input folder; file type is detected automatically
- Experiment Setup — name the run and choose an output folder
- Basecalling (POD5 only) — select a Dorado model and demultiplexing kit
- Filtering — choose a quality preset (Lenient / Moderate / Stringent) or set custom thresholds
- Analysis Options — pick the STR database (RefSeq or UCSC), set normalization cutoff, configure threads, enable optional SNV calling
- Review — confirm all settings
- Processing — live log and progress
- Results — browse summary tables, STR profiles, and allele plots
Results are saved to <output_dir>/<experiment_name>/:
<experiment_name>_YYYYMMDD_HHMMSS.log
4_analysis/
Countings/
Summaries/
barcode01_summary.tsv
barcode01_Profile.tsv
combined_summary.tsv
Plots/
barcode01_profile.png
Example output plot:
The pipeline includes 45 STR loci mapped to GRCh38, available in both RefSeq and UCSC coordinate systems. Select your preferred reference from the Analysis Options page.
Autosomal: CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D1S1656, D21S11, D22S1045, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, FGA, PentaD, PentaE, TH01, TPOX, vWA
Y-STR: DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, YGATAH4
The filtering options could be modified easily in the GUI. Some filtering presets are available for users.
| Preset | Dorado QS | Mean Q | Min Length | Accuracy |
|---|---|---|---|---|
| Lenient | 8 | 8 | ## bp | 0.80 |
| Moderate | 10 | 10 | ## bp | 0.85 |
| Stringent | 12 | 12 | ## bp | 0.90 |
For users who prefer to manage their environment manually:
pip install .Then install the required external tools separately:
| Tool | Purpose | Required |
|---|---|---|
| samtools | BAM handling | Yes |
| bedtools | Genomic intervals | Yes |
| minimap2 | Read alignment | Yes |
| dorado | Basecalling (POD5 input only) | Optional |
| xatlas | SNV calling | Optional |
| Rscript | Profile plots | Optional |
Note: dorado and xatlas are not available via conda. If you need basecalling (POD5 input) or SNV calling, install them manually from the links above. The pipeline will work without them — these features are simply skipped if the tools are not found.
This tool was developed at the Dubai Police Genome Center. MaSTRspy is inspired by STRspy, and we thank its authors for their foundational work.
Title
Mohammad S. Alsuwaidi1, Abdullah Albastaki1, Hanan Almulla1, Ahmed K. Omar1, Mohamed A. Almarri1,2
1 Genome Center, General Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai United Arab Emirates
2 College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
This project is licensed under the MIT License.