Software model
Methods, workflows, and utilities built around real genomics questions
Software development is part of the lab's research process. We prioritize biological relevance, reproducible execution, and performance on institutional and HPC-scale datasets.
01
Biological relevance
Tools are designed around active research needs in cancer genomics, assembly, long-read analysis, and comparative genomics.
02
Reproducibility
Workflows use versioned inputs, containerized execution, and portable pipeline structure whenever possible.
03
Performance
Methods are expected to remain practical on local servers, Kütral HPC, and large institutional datasets.
Catalog
Open pipelines and algorithms
Assembly and genome reconstruction
- Wengan for hybrid genome assembly.
- Fast-SG for alignment-free scaffolding graphs.
- FastKM for efficient k-mer matching.
- hic-scaffolding-nf for Hi-C scaffolding.
- k-count-nf for genome size estimation.
Cancer genomics
- purple-nf for somatic copy-number analysis.
- sv_somatic_cns for paired WGS structural variants.
- ampliconarchitect-nf for ecDNA detection.
- nf-gene-fusions for somatic mRNA fusions.
Reusable utilities
- alnsl for short-read WGS alignment.
- longreadstats for long-read QC.
- Container-first, HPC-ready patterns for production analysis.
Interested in using or adapting a workflow? Contact the lab to discuss the project and infrastructure context.