<p>&quot;DNA data&quot; comes in several forms dependent on the technology used to produce them.</p>
<p>Companies like 23andMe are using <a href="https://en.wikipedia.org/wiki/SNP_array" rel="nofollow noreferrer">SNP chips</a> and those are available for an only rather a limited number of species. To be completely honest, I don't even know what would be the raw data they would provide, but I would suspect it could be a vcf file.</p>
<p>If the chosen technology would be <a href="https://en.wikipedia.org/wiki/DNA_sequencing" rel="nofollow noreferrer">DNA sequencing</a>. DNA sequencing is provided by a few dozen of sequencing centres around the world, some of them associated with universities. DNA sequencing generates files that contain individual sequencing reads with assigned quality scores (&quot;how much the sequencer trusts each base&quot;), the typical formats are <code>fastq</code> (Illumina) or <code>.bam</code> (long read technologies). Usually, you would also need to find a suitable reference in one of the public databases, for instance, the <a href="https://www.ncbi.nlm.nih.gov/grc/human" rel="nofollow noreferrer">NCBI portal</a> for human reference. Then map your reads and do variant calling. Of course, then it depends on what would you be interested in.</p>
<p>If you don't care for your own DNA and you are more interested in life around you, you can check <a href="https://www.ncbi.nlm.nih.gov/" rel="nofollow noreferrer">ncbi</a> for all sorts of genomic data. If you would be interested to understand how the raw sequencing data work, <a href="https://www.ebi.ac.uk/ena/browser/home" rel="nofollow noreferrer">ebi</a> is a good place to look. Also, in every single paper generating/using sequencing data you there should be mention where in public databases you can find them.</p>
<p>Finally, let me warn you. Some of the genomic analyses are quite computationally heavy (not all though). If you don't have a specific question in mind, it would be wise to start with bacterial sequencing.</p>
<p>Hope you will have fun with DNA data!</p>

CC BY-SA 4.0
2021-02-11T18:45:53.407Z
2021-02-11T18:45:53.407Z
Kamil S Jaron
<p>Are you looking too far ahead into the future? No. This is certainly possible now. The gold standard being Illumina or BGI short read WGS. Long read sequencing can capture some extra data but is very noisy.</p>
<p>How or where do one obtain such DNA data? There are now many companies. You want one the uses NGS with reads at least 150 bp and garantees at least a mean of 30x read depth. In my opinion you also want one that gives you ownership of your data. Ideally they will give you; fastqs (raw reads), a BAM (mapped fastqs) and a VCF (variant file). I good company will ask you if you want to donate your data to science. Be warned these are not defaults. Many (most?) companies won't give you your raw data citing medico legal risk and then they will on sell it to a pharma companies. I think these guys are OK (as they are in Europe with good privacy laws) <a href="https://www.dantelabs.com/" rel="nofollow noreferrer">https://www.dantelabs.com/</a> but plz do your own research.</p>
<p>Last, these data could include info pertaining to your health and your family's health. Always good to speak to a genetic counsellor to understand these things.</p>

CC BY-SA 4.0
2021-02-12T10:49:40.720Z
My ownership is a big plus
John Greene
CC BY-SA 4.0
2021-02-11T20:49:09.857Z
2021-02-11T20:58:53.477Z
2021-02-11T20:58:53.477Z
Liam McIntyre
<p>As an end-user of my own data, specifically raw DNA sequence (WGS, whole genome sequencing). How or where do one obtain such DNA data so that a biology hobbyist can perform bioinformatics on this?</p>
<p>What keywords is best describe to the search engines when finding these online WGS websites).</p>
<p>It would be nice to have a USB stick mailed to me after such DNA HomeKit.  What file format is most commonly offered? (VCF?)</p>
<p>Am I looking too far ahead into the future?</p>

CC BY-SA 4.0
2021-02-11T16:50:43.927Z
Not sure if I follow, are you asking how or where you can get sequenced and what data you can expect when you would order such service?
Kamil S Jaron
CC BY-SA 4.0
2021-02-11T17:52:08.580Z
something that a home biology hobbyist can work with.
John Greene
CC BY-SA 4.0
2021-02-15T14:18:31.017Z
It is not clear to me where you wanna start. Do you have a biological sample or already extracted the DNA? What is your source organism? Is it a prokaryote or eukaroyte? What kind of bioinformatic task do you plan to do?
Mr_Z
<vcf><file-formats><wgs>
Obtaining Whole Genetic Sequence
# Obtaining Whole Genetic Sequence

(Asked by: username_0 on 2021-02-11)

As an end-user of my own data, specifically raw DNA sequence (WGS, whole genome sequencing). How or where do one obtain such DNA data so that a biology hobbyist can perform bioinformatics on this?

What keywords is best describe to the search engines when finding these online WGS websites).

It would be nice to have a USB stick mailed to me after such DNA HomeKit. What file format is most commonly offered? (VCF?)

Am I looking too far ahead into the future?

**Tags:** vcf, file-formats, wgs
> **Comments:**
> **username_1**: Not sure if I follow, are you asking how or where you can get sequenced and what data you can expect when you would order such service?  
> **username_0**: something that a home biology hobbyist can work with.  
> **username_2**: It is not clear to me where you wanna start. Do you have a biological sample or already extracted the DNA? What is your source organism? Is it a prokaryote or eukaroyte? What kind of bioinformatic task do you plan to do?  

---

## 2 answers

### Answer by username_3 on 2021-02-11. Score: 2 | Accepted answer

Are you looking too far ahead into the future? No. This is certainly possible now. The gold standard being Illumina or BGI short read WGS. Long read sequencing can capture some extra data but is very noisy.

How or where do one obtain such DNA data? There are now many companies. You want one the uses NGS with reads at least 150 bp and garantees at least a mean of 30x read depth. In my opinion you also want one that gives you ownership of your data. Ideally they will give you; fastqs (raw reads), a BAM (mapped fastqs) and a VCF (variant file). I good company will ask you if you want to donate your data to science. Be warned these are not defaults. Many (most?) companies won't give you your raw data citing medico legal risk and then they will on sell it to a pharma companies. I think these guys are OK (as they are in Europe with good privacy laws) <https://www.dantelabs.com/> but plz do your own research.

Last, these data could include info pertaining to your health and your family's health. Always good to speak to a genetic counsellor to understand these things.

> **Comments:**
> **username_0**: My ownership is a big plus  

---

### Answer by username_1 on 2021-02-11. Score: 3

"DNA data" comes in several forms dependent on the technology used to produce them.

Companies like 23andMe are using [SNP chips](https://en.wikipedia.org/wiki/SNP_array) and those are available for an only rather a limited number of species. To be completely honest, I don't even know what would be the raw data they would provide, but I would suspect it could be a vcf file.

If the chosen technology would be [DNA sequencing](https://en.wikipedia.org/wiki/DNA_sequencing). DNA sequencing is provided by a few dozen of sequencing centres around the world, some of them associated with universities. DNA sequencing generates files that contain individual sequencing reads with assigned quality scores ("how much the sequencer trusts each base"), the typical formats are `fastq` (Illumina) or `.bam` (long read technologies). Usually, you would also need to find a suitable reference in one of the public databases, for instance, the [NCBI portal](https://www.ncbi.nlm.nih.gov/grc/human) for human reference. Then map your reads and do variant calling. Of course, then it depends on what would you be interested in.

If you don't care for your own DNA and you are more interested in life around you, you can check [ncbi](https://www.ncbi.nlm.nih.gov/) for all sorts of genomic data. If you would be interested to understand how the raw sequencing data work, [ebi](https://www.ebi.ac.uk/ena/browser/home) is a good place to look. Also, in every single paper generating/using sequencing data you there should be mention where in public databases you can find them.

Finally, let me warn you. Some of the genomic analyses are quite computationally heavy (not all though). If you don't have a specific question in mind, it would be wise to start with bacterial sequencing.

Hope you will have fun with DNA data!


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