[DIYbio] Re: Best/Cheapest Services for DNA Sequencing & Synthesis

I think it really depends on what you are actually after.

Do you want just a sequenced genome(i.e. raw data)? A sequenced and assembled genome? Are you going to do library prep and DNA extractions? &c.

Here is a good primer for most of what you need to know about bacterial genome sequencing: https://peerj.com/preprints/453.pdf

For sequencing there are a number of places in the bay area that will pick up sequences from you and charge a few $ per sequence. At NASA we use Sequetech and some people at Biocurious use Elim Bio.

For DNA "barcoding" generally just using Sanger sequencing is the way to go. Most places give discounts if you are doing lots of samples.

For RNAseq, again it depends on how much work you want to do and what you want to do and who you trust. From what I hear Oregon State Core has really good prices for external users at ~$1500/ lane but I am sure local universities (Stanford) might also do something similar?

If you plan to do 16s (V3 or V4) microbiome sequencing I think Argonne National Lab in Illinois has the best prices in my not comprehensive but general search. That is if you plan to do analysis yourself and you have them do everything else(DNA extraction, library prep, sequencing). Here is a quote from an email chain that I had with Dr. Sean Gibbons, he has worked on lots of the popular press microbiome sequencing projects with Dr. Jack Gilbert at UChicago and Argonne:
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Here's a cost breakdown for Illumina MiSeq sequencing facility at Argonne:

DNA extraction: $14.25 per sample
PCR/library prep (16s): $6.63 per sample
1 MiSeq Sequencing Run (paired-end, 151X151 base pairs; can pool ~300 samples in one run): $2243.72

Therefore, if we assume 300 samples:

DNA Extraction: $4,275.00 (this is a step you could easily do yourself to save $$)
PCR and library prep: $1,989.00
Sequencing: $2,243.72

You can probably go cheaper by sequencing on an Illumina HiSeq. Also, I'm not sure what the prices are like at other facilities. I like Argonne because I get consistent results.


Thanks,
     Josiah Zayner


On Friday, August 14, 2015 at 10:46:59 PM UTC-7, Patrik D'haeseleer wrote:

Looks like Panellus stipticus is already sequenced though:

http://genome.jgi.doe.gov/Panst_KUC8834_1_1/Panst_KUC8834_1_1.info.html

Patrik

On Friday, August 14, 2015 at 12:15:48 PM UTC-7, Koeng wrote:

"Idea: Community effort genome seq?

Andreas, our friend on the list, recently asked about using the Oxford Technologies Nanopore. I reached out because the lab I work for does have a Nanopore MiniIon. He proposed sequencing thePanellus stipticus genome to determine how to synthesize the fungal luciferase. I don't know if the sequence is publicly available or not. I like his proposal but I will have to convince the boss to carry this out. I don't really know how similar the Nanopore is to the Ion Proton NGS platform, in terms of cDNA library preparation or data analysis. It will be wonderful if the community came together to sequence an organism. I don't know how it can be done. If we can sequence the genome and make it public, I think it will be a big step for DIYbio. Time is of the essence for me."

This is pretty relevant^ and could probably be easily done.

-Koeng
On Thursday, August 13, 2015 at 12:57:35 PM UTC-7, Patrik D'haeseleer wrote:

Speak of the devil - I just got an email promotion through ScienceExchange for de novo genome sequencing and assembly for $1500 per sample, at a sequencing depth of 100x for smaller genomes (up to 5Mb).

That's definitely more expensive than it needs to be, considering how many of these you could multiplex on a single Illumina run, but as far as I know that's still the lowest (or *only*?) published rate for bacterial genome sequencing. And entirely feasible for a DIYbio lab with a little crowdfunding. For that price, they do handle all the multiplexing and demultiplexing logistics, and provide genome assembly as well.

Here's the email I got, complete with discount code at the end:

De novo Assembly of Novel Genomes: $1,500 per Sample At 100x Coverage
Next generation sequencing technologies provide high genome coverages at a relatively low cost. However, due to limited read lengths, de novo assembly often leaves gaps or fails to distinguish circular genomes from linear. myGenomics can help you fill this gap by combining standard library prep (PE100) with a single (3-5Kb) mate-pair library followed by sequencing at high depth coverage all for a special promotional price of $1,500 per sample. The mean sequencing depth coverage for this service is >100x for smaller genomes (up to 5Mb). Sequencing is performed on an Illumina platform and data analysis of an assembled genome (FASTa file) is included.

Experienced Team of Ph.D Scientists
myGenomics is a CLIA lab that specializes in next generation sequencing and is based in Alpharetta, Georgia in the United States. All work is done on site to ensure the highest quality and the fastest turnaround possible.    

Easy to Submit Samples and Get Results
Please send a sample of 1-5 μg high-quality human DNA, blood or saliva samples packed with blue ice packs. The turn-around time is 20-30 business days. Data analysis if needed is available for $200/sample and will deliver VCF (variant call file), CNV and cnLOH reports with BWA mapping and GATK variant call information. Included filters are variant allele frequency (1000 genome), known pathogenic variants (dbSNP) and suspect variants (frameshift, stop gain, stop loss), SIFT score, Polyphen score.  You will also receive various deliverables such as sample QC, fragmentation QC, library prep QC, raw data (FASTq files), sequencing reads QC, coverage and FastQC plots.

Redeem This Offer
To start, simply request a quote and include the promotion code "NovelGenome-mG" in the Promotion Code field of your request. A volume discount is available for >10 samples. The offer ends at the end of September, but you just need to request a quote to qualify. You can work with the lab members on the project after this date.  

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