Thinking about whole genome storage, the human genome is 3.2 Gbp in size. That's a base-four data-type, if you discount methylation and other forms of chemical DNA modification.
However, how do they encode that to binary? Do they store as ASCII, which (if memory serves) uses a full byte to store each character? Because encoding a base-four datatype like a/c/t/g to binary 1/0 could be minimised to only two bits per base, meaning that storing 8 bits per base (ASCII or similar) would be inflating the data 4x, making your 3.2 Gbp genome occupy 3.2 Gb instead of a minimum of 0.8 Gb before compression?
Or am I wildly off the mark? :)
That accounts only for the actual base sequence of course; your annotations etc. will still outstrip the DNA vastly in size, although they will probably have a better compression ratio.
Has anyone looked into a direct basepair->bit codec for minimisation of genome storage? Even a compression from a full byte per base down to four bits would halve storage size while leaving plenty of overhead for modified bases etc.?
A bit of a speculative post into the future. Reading about new ventures into exome sequencing and data amounting to >6GB just for the base pairs, I was curious about the media formats that are used, such as DVDs. A couple articles got me thinking about full genome sequencing (3x10^9 base pairs and about 50TB of storage), would be possible on several 4Terabyte HDDs, but terabyte (1-15TB) optical discs like ones by Fujifilm may make portable genomic data a lot simpler to handle. A few links I found on it:
http://fudzilla.com/home/item/29581-1tb-optical-discs-coming-in-2015
http://www.tweaktown.com/news/26908/1tb_optical_discs_are_coming_but_you_ll_have_to_wait_until_2015/index.html
http://news.yahoo.com/1-000-genome-almost-ready-111300774.html
http://www.genomeweb.com/clinical-genomics/23andme-opens-research-portal-outside-investigators-effort-advance-genomics-know
http://www.wired.com/wiredscience/2012/11/social-codes/
http://www.kinexus.ca/pdf/graphs_charts/HumanGenomeSequence.pdf
I guess if full genome sequencing is available, the most practical storage medium would be one that doesn't comprise a major part of the cost of sequencing. I think the cost of TB discs, like Blu- ray, and DVDs before them, might be as little as $0.20- few dollars each, but their price might not be as low if TB discs have popular adoption, which would come with UltraHD cinema discs for 4K resolution televisions and Playstation 4 discs (if they exceed 25-50GB). The idea of an entire genome fitting on just a few optical discs instead of 50 is actually a little encouraging.
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