MindExpansion Posted February 8, 2015 Hi guys, I'm putting this out there but I'm looking for someone with access to and skill to undertake genotyping/sequencing of Aus fungal specimens. If you have access to such facilities or know of someone who does, please get in touch. Peace, Mind Share this post Link to post Share on other sites
Darklight Posted February 8, 2015 I enquired about this a fair while ago, not sure if the technology has changed in the last 12 months, here's a mashup of what I got back then You can split your sequencing into 3 stages. You'll need a wet lab to extract the DNA. It's not hard, tho some ppl do it better than others Cheap and local is available for most people, obtainable for beer in some instances. The sequencing mob will want about 5ug of high quality DNA per species, which is a lot. A crude prep won't pass the sequencing company's QC either. Find a company to do the sequencing DNA can be shipped anywhere in the world ( AFAIK, no restrictions exist on import or export )- find the cheapest and most reliable sequencing place Cheapest a few years ago were the BGI Beijing Genome Institute, AGRF and The Ramaciotti Centre, UNSW. If you are linked in with geneticists who have the relevant toys, sometimes there will be a run done with a spare 'lane' free- ie they aren't running a fully stocked session and have space for your species, in which case it will cost fuckall in comparison to BGI etc above Whoever you choose will want to know How big is the genome?Is there a closely related species that could be used as a reference genome?How much coverage do you want? Eg how many times is each base represented by a read. For example, wheat and barley are appox 5.5Gb and about 8x coverage. .What kind of library preparation? I would suggest (on an Illumina instrument) 75 or100bp paired end reads, AND a 3-5kb mate pair library. Paired end reads are cheap and will give you lots of coverage. A mate pair library is critical to putting a genome together if there is no reference genome.They may ask more technical questions relevant to the sequencing You will also need bioinformatics support to make sense of your data I'm under the impression it takes a lot of computing power and storage space, and that human expertise is important in interpreting the data. I got pretty lost after the bits requesting info on coverage. Roundabout then I gave up and decided to delegate the job to someone else when it came up Not sure if this is what you are after, good luck. It's all very do-able, but it's not as simple as it looks on CSI unless you are willing to throw $$$ at it, or have genetically obsessed mates Share this post Link to post Share on other sites
Darklight Posted February 8, 2015 What species are you looking at having sequenced? I was looking at a few too. Perhaps we could share costs? Share this post Link to post Share on other sites
