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

"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.  

...