Seqpipe is a small software engineering studio in Sofia, Bulgaria, building bioinformatics platforms for genomics research teams. Current focus is GAIn (Genomic Annotation Infrastructure) — a framework for reproducible variant annotation across hg19, hg38, and T2T-CHM13 (manuscript in preparation). Long-running platform collaboration with research groups at Cold Spring Harbor Laboratory on GPF (Genotypes and Phenotypes in Families), the platform that runs the SFARI autism cohort (Genome Research, 2025).
Projects
GAIn — Genomic Annotation Infrastructure
Current · manuscript in preparation · with the Iossifov lab at Cold Spring Harbor Laboratory
Framework for transparent, reproducible variant annotation. Curated Genomic Resource Repository of 200+ version-pinned resources across hg19, hg38, and T2T-CHM13. Declarative YAML pipelines, Python plugin annotators (Ensembl VEP and SpliceAI integrations included). Selective re-annotation: when a resource updates, GAIn recomputes only the affected columns. CLI parallelizes onto SGE / SLURM.
Stack: Python · Dask · DuckDB · Docker · SGE / SLURM
gain.iossifovlab.com ·
grr.iossifovlab.com ·
github.com/iossifovlab/gain
GPF — Genotypes and Phenotypes in Families
Since 2014 · with the Iossifov lab at Cold Spring Harbor Laboratory
Platform for managing and analyzing genetic variants and phenotypic data from family-based cohorts. Powers the SFARI autism cohort analysis at Cold Spring Harbor Laboratory. Pluggable storage backends (DuckDB, Apache Impala / Hadoop, BigQuery). Published in Genome Research (2025).
Stack: Python · Django · Angular · DuckDB · Apache Impala · BigQuery
github.com/iossifovlab/gpf
s-GAINS — Sparse Genomic Analysis of Individual Nuclei by Sequencing
2017–2020 · with the Krasnitz lab at Cold Spring Harbor Laboratory
Single-cell CNV profiling pipeline — from NGS read alignment through to data preparation for visualization. Contributed to Cancer Research (2018) and JCO Clinical Cancer Informatics (2020).
Stack: Python · NumPy · pandas · pysam · Bowtie · samtools
github.com/KrasnitzLab/sgains
SCclust
With the Krasnitz lab at Cold Spring Harbor Laboratory
Segmentation and clustering of single-cell sequencing copy-number profiles. Feature selection based on breakpoints; permutation-based FDRs for Fisher test p-values; clone-structure identification.
Stack: R · Bioconductor
github.com/KrasnitzLab/SCclust
SCGV — Single Cell Genome Viewer
With the Krasnitz lab at Cold Spring Harbor Laboratory
Interactive visualization tool for single-cell genomics data, with emphasis on cancer. Joint and individual examination of DNA copy-number profiles across cells harvested from multiple anatomic locations.
Stack: Python · PyQt
github.com/KrasnitzLab/SCGV