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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Seqpipe — Bioinformatics platforms for genomics research</title>
<meta name="description" content="Seqpipe is a small software engineering studio in Sofia, Bulgaria, building bioinformatics platforms for genomics research.">
<meta name="author" content="Seqpipe">
<link rel="shortcut icon" href="images/favicon.ico">
<link rel="stylesheet" href="css/styles.css?v=2.0">
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<main>
<header>
<h1>Seqpipe</h1>
<p class="tagline">Bioinformatics platforms for genomics research.</p>
</header>
<section class="intro">
<p>
Seqpipe is a small software engineering studio in Sofia, Bulgaria, building bioinformatics platforms for genomics research teams. Current focus is <strong>GAIn (Genomic Annotation Infrastructure)</strong> — a framework for reproducible variant annotation across hg19, hg38, and T2T-CHM13 (manuscript in preparation). Long-running platform collaboration with research groups at <strong>Cold Spring Harbor Laboratory</strong> on <strong>GPF (Genotypes and Phenotypes in Families)</strong>, the platform that runs the <strong>SFARI</strong> autism cohort (<em>Genome Research</em>, 2025).
</p>
</section>
<section class="projects">
<h2>Projects</h2>
<article>
<h3>GAIn — Genomic Annotation Infrastructure</h3>
<p class="meta">Current · manuscript in preparation · with the Iossifov lab at Cold Spring Harbor Laboratory</p>
<p>
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.
</p>
<p class="stack">Stack: Python · Dask · DuckDB · Docker · SGE / SLURM</p>
<p class="links">
<a href="https://gain.iossifovlab.com">gain.iossifovlab.com</a> ·
<a href="https://grr.iossifovlab.com">grr.iossifovlab.com</a> ·
<a href="https://github.com/iossifovlab/gain">github.com/iossifovlab/gain</a>
</p>
</article>
<article>
<h3>GPF — Genotypes and Phenotypes in Families</h3>
<p class="meta">Since 2014 · with the Iossifov lab at Cold Spring Harbor Laboratory</p>
<p>
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 <em>Genome Research</em> (2025).
</p>
<p class="stack">Stack: Python · Django · Angular · DuckDB · Apache Impala · BigQuery</p>
<p class="links">
<a href="https://github.com/iossifovlab/gpf">github.com/iossifovlab/gpf</a>
</p>
</article>
<article>
<h3>s-GAINS — Sparse Genomic Analysis of Individual Nuclei by Sequencing</h3>
<p class="meta">2017–2020 · with the Krasnitz lab at Cold Spring Harbor Laboratory</p>
<p>
Single-cell CNV profiling pipeline — from NGS read alignment through to data preparation for visualization. Contributed to <em>Cancer Research</em> (2018) and <em>JCO Clinical Cancer Informatics</em> (2020).
</p>
<p class="stack">Stack: Python · NumPy · pandas · pysam · Bowtie · samtools</p>
<p class="links">
<a href="https://github.com/KrasnitzLab/sgains">github.com/KrasnitzLab/sgains</a>
</p>
</article>
<article>
<h3>SCclust</h3>
<p class="meta">With the Krasnitz lab at Cold Spring Harbor Laboratory</p>
<p>
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.
</p>
<p class="stack">Stack: R · Bioconductor</p>
<p class="links">
<a href="https://github.com/KrasnitzLab/SCclust">github.com/KrasnitzLab/SCclust</a>
</p>
</article>
<article>
<h3>SCGV — Single Cell Genome Viewer</h3>
<p class="meta">With the Krasnitz lab at Cold Spring Harbor Laboratory</p>
<p>
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.
</p>
<p class="stack">Stack: Python · PyQt</p>
<p class="links">
<a href="https://github.com/KrasnitzLab/SCGV">github.com/KrasnitzLab/SCGV</a>
</p>
</article>
</section>
<section class="contact">
<h2>Contact</h2>
<p>
Lubomir Chorbadjiev — <a href="mailto:lchorbadjiev@seqpipe.com">lchorbadjiev@seqpipe.com</a><br>
Sofia, Bulgaria<br>
<a href="https://linkedin.com/in/lchorbadjiev">linkedin.com/in/lchorbadjiev</a>
</p>
</section>
</main>
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