Nucleus Genomics whole-genome data
What your Nucleus downloads contain, and what to do with them
Nucleus sequenced you at 30x and lets you download the genome as a VCF, CRAM, SV, CNV or FASTQ file. Its own reports lean on polygenic scores across a very large number of conditions. Two of those files can also be read the other way: a fixed, named panel, attributed to its sources, with a record of what was covered.
Get both · €169 See a sample report first
€89 for the full report from your VCF · €109 for the Deep Read panel from your CRAM · €169 prepaid together.
The five downloads
Nucleus's FAQ says you can "download your whole genome as VCF, CRAM, SV, CNV, or FASTQ file types" from the account settings page, and separately as a file "formatted for upload to sites like Promethease or GEDmatch". Its health test is "whole-genome sequencing to read your DNA at an average of 30X coverage". Here is what each download is, and which ones matter here.
- The VCF is the list of positions where you differ from the reference, usually well under a gigabyte. It is the file for the €89 full report: clinical findings, carrier status, the pharmacogenes a VCF can carry, traits, ancestry and the polygenic scores.
- The CRAM is the aligned reads in compressed form, the equivalent of the BAM other providers ship. It is the file for the €109 Deep Read panel. A CRAM is written against one exact reference assembly and can only be decoded with that assembly; the file check reads which one yours needs and says whether we hold it, before you pay.
- The SV and CNV files are Nucleus's own structural-variant and copy-number calls. We do not read them. Deep Read measures copy number directly from the reads for the genes where it matters, CYP2D6 above all.
- The FASTQ is the unaligned raw reads. We do not use it. Keep it; it is the only file from which everything else can be rebuilt.
- The Promethease/GEDmatch export is a chip-style genotype list derived from the genome. It is the least of the five. Upload the VCF instead; it carries everything the export does and a great deal more.
Nucleus does not state on its pages which reference build its files are on. Nothing is asked of you: the file check reads the build from the header, and a GRCh37 file is lifted to GRCh38 before analysis. A GRCh38 VCF is usually ready in about a quarter of an hour; a large GRCh37 file can take a couple of hours.
What a second reading adds
Nucleus's reports are one interpretation, with a strong emphasis on polygenic risk. This one is built differently, and the difference is the product. The panel is fixed and named: every gene, condition and trait examined is on one page before you pay. Every finding is attributed to the source it was restated from, and the version of each source, ClinVar, ACMG SF and CPIC among them, is printed on the report. And the report keeps what it found apart from what it could examine: a variant-only VCF cannot tell "you are clear" from "nobody looked", so a clean result from it is reported as absent, never as examined and clear.
The CRAM changes that. Deep Read counts the bases covered at 10x or better across the whole report panel, so each gene comes back examined, partly examined, or not measured. The same reads drive the 29-gene pharmacogenomic panel to CPIC star-allele resolution, and a one-page hand-off you can take to a prescriber. Where the reads are too thin for a gene, the panel declines that gene rather than calling it. We carry six polygenic scores, chosen because they hold up on a Finnish file, and we will not race anyone on the count.
Who Nucleus is
Nucleus Genomics is a New York company founded in 2021. Its launch announcement in March 2024 put the 30x kit at $399 with a $39-a-year membership for new features, and named a CLIA-certified, CAP-accredited laboratory in North Carolina; its health test page lists the kit at $499 today. Its terms say that if you close your account "we will not retain any information or data" beyond what the law requires, so download your files before you do. As with every provider on these pages, the copies you hold are the ones you control.
How to get your files out of Nucleus
- Sign in and open Account settings, or choose Downloads from the account menu, as Nucleus's FAQ describes.
- Download the VCF first. It is the small file and the one the full report needs.
- Download the CRAM and its index (
.crai) if you want the Deep Read panel. It is large; give it a wired connection. - Upload them here as delivered. Do not rename, unpack or convert them.
Nucleus's products and download process are described from its public pages on 3 September 2026 and may change. We do not speak for Nucleus.
Your files do not leave the EU
Processing and storage are in Finland, under GDPR Article 9 special-category protection, and nothing crosses an EU border. The VCF you upload is deleted after analysis by default; the reads are deleted the moment the Deep Read run finishes, whether it succeeded or failed. With your consent, and only if you want re-analysis later, we keep a small normalised variant file that you can delete from your dashboard at any time. Security & your data.
Check a Nucleus file before you pay
Drop the VCF or the CRAM below. It is read inside this page, on your own device: nothing is uploaded, no account is needed, and you get back the format, the reference build and what report it supports.
Read on your device, not ours. Your file is never uploaded and no account is needed. We are a genomics company telling you not to send us your genome yet, and that is deliberate. Security & your data →
Reading on your device…
That's . We can build your report from it.
What it can tell you
What it can't
A chip reads a fixed set of common spots, so the rare-variant panels need a sequenced genome. We tell you this now rather than after you have paid.
One-time, yours to keep. Your file is still on your device: you upload it after checkout, over an encrypted connection, to storage in Finland.
That's : aligned reads.
This is exactly what the Deep Read pharmacogenomic panel needs: 29 targets read at base level, including the CYP2D6 star-alleles a normal VCF cannot reliably call. The standard report is built from a VCF/gVCF, so aligned reads sit alongside one rather than replacing it.
Deep Read needs standard-depth reads. A low-pass file, MyHeritage's own sequencing download among them, is read about twice over rather than thirty times, which is too thin to call these genes from. We measure the depth and stop rather than guess.
A CRAM also needs the exact reference assembly it was compressed against, not merely the same genome build. We hold the common ones and check yours before taking any money, so an assembly we cannot read is refused rather than charged for.
What the pair covers
The bundle is the whole-genome report plus the Deep Read panel. The report is built from a variant file and the panel from your reads, so it takes both. Most sequencing providers hand you both in the same download.
Nothing was uploaded, and you have not paid anything. We would rather turn a file away here than sell you a report it cannot support.
This check ran on your device from your file's header. We confirm the full file after upload, and never charge for a report we cannot build.
Common questions
The full report from your VCF plus the Deep Read panel from your CRAM is €169, prepaid together. Both reports are yours to keep.
Sequenced elsewhere? Dante Labs files · Nebula and DNA Complete files · Sequencing.com files · What your reads add, whoever sequenced you