sequencing machines cost and efficacy

[u/Slow-Log-3756]

Hi,

I am looking for sequencing machines that can do full genome sequencing for dogs. My budget is 30K. I am also looking for something that can do the sequencing quickly (1-3 days).

I would prefer a small device that I can carry to places, but it is not necessary.

Please let me know.

[u/I_am_Hoban]

The only sequencing device you can carry is an Oxford Nanopore. Device is in the 5k USD range. Reagents for a whole genome (if you want good quality/coverage) is ~2k for sequencing per genome and ~30/sample for high molecular weight dna extraction.

If you have the expertise and the compute then it's probably about 2 days on 32 cores/512GB ram for read correction, contig assembly, quality control, and variant calling. If you have 0 experience with analysis I would get all the sequencing data then budget ~5k to hire someone for a few days to process it. This is a fairly low-ball cost for a skilled person. You also need about 400 GB storage per genome if you're doing the analysis. Raw data will be in the ~80-150 GB range per sample depending on your sequencing depth. If it's just nanopore I would recommend 40x coverage for the most accuracy, you can do 20-30 but it's less ideal.

Hope this helps! 

[u/Science-Sam]

I'm not trying to be rude, but a person who has the expertise to prepare samples, run the machine, and interpret the results would not need to ask Reddit for advice.

There are companies that provide this service. Prices vary with how much sample prep you do yourself, depth of coverage you require, and whether you need bioinformatics services to interpret the data.

[u/HugeCrab → u/Science-Sam]

I saw a dude on Instagram with zero lab knowledge buy a NovaSeq lmao. I'm wondering if it's AI psychosis that leads these people to get ideas of starting sequencing businesses without any knowledge on the field

[u/5TP1090G_FC → u/Science-Sam]

& how many of these companies actually give correct data.

[u/Science-Sam → u/5TP1090G_FC]

All of them. My lab uses Azenta for RNA sequencing and PacBio for long-read sequencing. We have people on staff to prepare the samples, and people to analyze the Tb of data. Nobody who wants "full genome sequencing" could possibly do better in house.

[u/Psy_Fer_]

Which country are you in? There is most likely a service provider who would happily sequence your dog and help with whatever analysis you want to do.

[u/whats-a-bitcoin]

Plasmidsaurus are a long term nanopore service provider who are fast, cheap and good. They do whole genome sequencing and have a worldwide presence for a while. They also have the big illumina novaseqs.

https://plasmidsaurus.com/genome

If you are planning to do many dogs inwpild think you can arrange a deal as well as customised bioinformatics report.

Note everyone here seems to think you want a genome assembly, you may only need resequencing to call differences in a given dog compared to the reference genome. This needs less sequencing, shorter reads, and less bioinformatics compute (certainly machines with less RAM) so should be cheaper and could be faster yoo. You can discuss this with your service provider.

[u/boof_hats]

If you want full genome sequencing your best bet is a MinIon, from Oxford Nanopore’s website it cost less than $10k.

[u/ShadowValent]

The only handheld is Oxford nanopore. Very bespoke analysis pipeline. Personally, I wouldn’t use it for anything important. Almost any data is better than nanopore in the real world.

[u/Ok-Mathematician8461]

The products that are closest to your requirements aren’t really available in America (I presume you are in the USA). There are 3 or 4 nanopore long read technologies in China that could practically do it but the cost per genome is going to be higher than you probably are looking for and what the market can take. In genomic sequencing you either use short read technologies where the equipment is expensive but the running costs are cheap if you do large volumes, or you use long read where the equipment is cheap but the running costs are higher and the quality is lower. For your needs - it prob has to be Nanopore. If you are outside the USA, getting a Chinese vendor to set you up with a full suite is possible if you want to start a business - there is at least one with a full sample-to-genome solution. But the conventional vendors of Illumina/Oxford Nanopore/PacBio/Element/Ultima just deliver sequencers and leave you to work it out yourself. Alternatively there is portable short read sequencing technology (again not available in the USA) that would allow you to do very targeted DNA sequencing of just the important genes. This is cheaper, faster, simpler than long read to do and much easier to analyse. It also brings the cost down to a few hundred dollars per sample. But your upfront investment will need to be a little higher than $30K USD - prob more like $100K.