RNA sequencing analysis using STAR, RSEM, HISAT2 and extensive QC.
Cortessa helps researchers, labs, and early-stage biotech teams analyze data, communicate findings clearly, and present their work credibly online — backed by published research and open-source tools with real usage.
We don't sell templates or generic execution. We sell judgment — the difference between an analysis that looks right and one that is right.
Most researchers aren't short on software — they're short on someone who can look at a result and tell them whether to trust it.
Raw FASTQs, half-labeled sample sheets, no documented QC — cleanup eats the timeline before the real question even gets asked.
A plot with no judgment behind it can't tell you whether a result reflects real biology or noise in the dataset.
Without a plain-language interpretation you can stand behind, results sit in a folder instead of a manuscript, a committee meeting, or a pitch.
Each module can stand alone — but most clients start with analysis, and grow into the rest once trust is established.
RNA-seq and NGS analysis, statistics, and publication-ready figures — with a written interpretation, not just a script output. Delivered as a report or a reproducible notebook, your choice.
Replaces vague claims with precise scientific language that a reviewer or investor can actually evaluate — the same standard of precision as the analysis itself, applied to how it's written.
A website that reads the way a real lab page should: publications pulled in automatically and correctly, research interests described the way a scientist would say them — not boilerplate agency copy.
Every analysis follows a defined, defensible workflow — not a black box. Pick an assay type below and watch each stage run.
RNA sequencing analysis using STAR, RSEM, HISAT2 and extensive QC.
Variant calling and annotation from WGS and targeted sequencing.
Single-cell RNA-seq pipelines for barcode-based protocols and modern aligners.
Assembly and binning workflows for metagenomic datasets.
ChIP-seq peak calling, QC and downstream analysis.
Amplicon sequencing analysis with validated QC and reporting.
Nanopore demultiplexing, QC and alignment workflows.
ATAC-seq peak-calling and chromatin accessibility analysis.
Reproducible ancient DNA analysis from raw reads to results.
Use established nf-core workflows where they fit the biological question — versioned, community-maintained infrastructure rather than a one-off script stack.
Pipeline versions, parameters and outputs stay tied to the same analysis so another run can be understood and reproduced.
When no existing workflow fits, custom notebooks and analysis code extend the stack without pretending every problem is the same.
Computation is only the middle of the process. QC, figures and biological interpretation are what make the output useful.
The point is not to build another platform. It is to combine proven scientific infrastructure with careful interpretation and a deliverable a researcher can actually use.
Use established workflows where they fit. Build custom analysis where they don't. Always connect the computation back to the biological question.
Use established Nextflow workflows such as Sarek and RNA-seq where they fit the question — versioned, reproducible, and easier to audit than a one-off script stack.
Pipeline versions, parameters, notebooks, figures, and interpretation stay tied to the same analysis rather than becoming disconnected files.
QC is not the finish line. Results are checked for whether they support the biological question before they become a finding.
Publication-ready figures and a plain-language interpretation turn a technically correct output into something usable in a manuscript, meeting, or pitch.
When an existing workflow does not fit the question, custom notebooks and analysis code extend the analysis without forcing every problem into the same pipeline.
For the separate website offer, publications, research interests, and workflow explanations are structured for scientific credibility rather than generic agency polish.
Every entry here is independently verifiable — not portfolio copy.
Three open-source packages, 7,000+ combined downloads — three sole-author preprints — one live example of the website module.
A Python package that resolves gene identifiers across naming conventions and databases, cutting out one of the most common friction points in cross-dataset analysis.
View on PyPI →A tool for working with Phred quality scores in sequencing data, built to speed up a routine but essential step of NGS quality control.
View on PyPI →A package for evolutionary motif analysis, used to identify and compare conserved sequence patterns across genomic datasets.
View on PyPI →Sole-author analysis integrating multiple omics layers within the TCGA breast cancer cohort to characterize patterns across the dataset.
Read preprint →A multi-omics investigation into MEF2C haploinsufficiency, examining its molecular signatures independently, sole-author, start to finish.
Read preprint →Whole-genome sequencing analysis of the HCC1395 reference cell line, characterizing somatic variation with a fully reproducible pipeline.
Read preprint →A demonstration build of the Module 3 offering: auto-synced publications feed, clean research-interest framing, and an example workflow layer — no generic template filler.
No account managers, no subcontracted analysts. When you work with Cortessa, you work directly with the person who runs the analysis.
Hi, my name is Taha Ahmad.
I graduated in Biology from METU and am currently pursuing an M.Sc. at TUM School of Life Sciences. Along the way, I've gained experience across both academia and industry, working on projects in computational biology, bioinformatics, biotechnology, and scientific software development, including R&D at Ankara University Biomedical Engineering and industry experience at BIOMATEN, METU's biomaterials research center.
I started Cortessa because I genuinely enjoy using computation to solve biological problems. Whether it's analyzing sequencing data, building reproducible workflows, developing scientific software, or creating research-focused digital platforms, my goal is always the same: to deliver work that is technically sound, practical, and genuinely useful.
Cortessa is an independent consultancy, and every project is handled personally—from the initial discussion to the final deliverables. I intentionally take on a limited number of projects so that each client receives the time, attention, and quality their work deserves.
A clear starting price for a defined analysis scope. Larger or more complex projects are quoted separately.
The $300 package covers the defined starter scope above. Larger, multi-dataset, or custom projects are quoted separately before work starts.
Price and timeline are worked out together after a short conversation about what you need — same fixed-scope principle, just sized to a bigger project.
No open-ended hours. You know the scope and the price before we start.
Send the dataset and the question you're trying to answer — no need to pre-clean it.
A flat price for a defined deliverable, confirmed before any work begins.
QC, analysis, and publication-ready visuals delivered within about a week.
A written interpretation so the result is usable, not just technically correct.
Cortessa is deliberately narrow. That's not a limitation — it's the point.
Cortessa is a research-use service, not a data-hosting platform. Handling, access, retention, and deletion are agreed before analysis begins.
Client datasets are accessed only for the agreed analysis and are kept separate from unrelated projects.
Client data is not reused for unrelated projects or purposes.
Storage and deletion expectations are agreed at project start rather than leaving files indefinitely by default.
Clients remain responsible for the permissions and authorizations required for the data they provide. Clinical or diagnostic use is outside scope.
Just tell us upfront — most academic clients pay via a lab purchase order or invoice rather than a personal card. We'll confirm your institution's process before quoting, and issue a formal invoice that fits it. If your university's PO process takes a few weeks, we'll plan the timeline around that rather than assuming a same-week start.
Yes. QC and preprocessing are part of the Analysis Starter Package, not a prerequisite for it. Send the data as it exists — raw, messy, partially labeled — and the cleanup happens as step one, not something you need to solve before reaching out.
Yes, happily, especially for unpublished data or pre-patent work. It's normal to ask, and we'll sign before any dataset changes hands if you'd like one in place.
Most commonly RNA-seq and other NGS data (FASTQ, BAM, count matrices), along with standard tabular formats (CSV, TSV, Excel) for other omics or experimental data. If you're not sure your format is supported, ask — it's a five-minute answer either way.
Yes. Every project can be delivered as a written report, a reproducible notebook containing the actual code, outputs, and Explanatory notes, or both — whichever is more useful for how you plan to use the results. Just mention your preference when we scope the project.
No — Cortessa is a personal service, not a hosted product. Tools are used internally to deliver analysis and writing faster and more clearly, but there's no software you log into and no data sitting on a shared platform. Your files stay with you and with the person actually doing the work.
That happens, and it's not a failure — it's often the actual finding. The written summary will say so plainly, and one round of clarifying revisions is included if you need the analysis extended or re-framed around a follow-up question.
No — this is a paid service, not a collaboration seeking authorship. If your contribution standards call for acknowledgment given the scope of analytical work involved, that's entirely your call to make.
Yes — all work is remote, and most communication happens over email or a short call. Time zones are rarely an issue given the project turnaround is measured in days, not hours.
Then you'll be told that directly, ideally before any money changes hands. Generic web design, marketing work, and open-ended consulting are explicitly outside scope — see the section above — and it's more useful to say so early than to take on a project outside real expertise.
Tell us what you're working with — we'll tell you honestly whether we're the right fit.
Tell me what you have, what you are trying to answer, and where you are stuck. I will tell you directly whether Cortessa is the right fit.