4 ms·

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ ~800MB for human genome

by xaa 14y ago

hyperbovine 14y ago
That is roughly the size needed to represent 3.3 billion ACTGs , however sequencer output is much larger since each base is sequenced many times, and accompanying metadata (quality information) is also included. File sizes for current sequencer output is on the order of 100-300gb compressed. It's big enough to create real roadblocks when you are trying to do analysis.
- Retric 14y ago
  It can also end up well below 800MB per person if you encode it as known sequences of DNA + tiny new random variations.
  - hyperbovine 14y ago
    True, but in order to do that you have to know what the new random variations are. Output from existing sequencers, as well as the current crop of algorithms, are not good enough to do that with high confidence. Thus, people tend to keep everything. You can get some gain by doing reference-based compression, but you're still looking at on the order of 100s of gb per sample.
tomkinstinch 14y ago
When compressed relative to a reference genome, you can get a ~2.9Gbp human genome down to ~3.3MiB of data[1]. Sequences are actually pretty compressible in general, owing to conservation of functional domains and repeats. Data from next-gen sequencers have many small overlapping segments though, so the raw output takes up MUCH more space. By the way, for anyone looking for more information about some of the methods currently being used for sequencing (Illumina, 454), check out these videos from the WUSTL Genome Center: http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/nextgen_video_tour http://gep.wustl.edu/curriculum/course_materials_WU/introduc... They don't cover Ion Torrent, which is unfortunate because it is way cool. gourneau can probably point to a better video, but here are a couple for Ion Torrent: http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=yVf2295JqUg http://www.youtube.com/watch?v=yVf2295JqUg ...and the Nature paper: http://www.nature.com/nature/journal/v475/n7356/full/nature10242.html http://www.nature.com/nature/journal/v475/n7356/full/nature1... 1. http://dhruvbird.com/genome_compression.pdf http://dhruvbird.com/genome_compression.pdf

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ ~800MB for human genome

by xaa 14y ago

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ ~800MB for human genome

hyperbovine 14y ago

That is roughly the size needed to represent 3.3 billion ACTGs , however sequencer output is much larger since each base is sequenced many times, and accompanying metadata (quality information) is also included. File sizes for current sequencer output is on the order of 100-300gb compressed. It's big enough to create real roadblocks when you are trying to do analysis.

Retric 14y ago
It can also end up well below 800MB per person if you encode it as known sequences of DNA + tiny new random variations.
- hyperbovine 14y ago
  True, but in order to do that you have to know what the new random variations are. Output from existing sequencers, as well as the current crop of algorithms, are not good enough to do that with high confidence. Thus, people tend to keep everything. You can get some gain by doing reference-based compression, but you're still looking at on the order of 100s of gb per sample.

tomkinstinch 14y ago

When compressed relative to a reference genome, you can get a ~2.9Gbp human genome down to ~3.3MiB of data[1]. Sequences are actually pretty compressible in general, owing to conservation of functional domains and repeats. Data from next-gen sequencers have many small overlapping segments though, so the raw output takes up MUCH more space. By the way, for anyone looking for more information about some of the methods currently being used for sequencing (Illumina, 454), check out these videos from the WUSTL Genome Center: http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/nextgen_video_tour http://gep.wustl.edu/curriculum/course_materials_WU/introduc... They don't cover Ion Torrent, which is unfortunate because it is way cool. gourneau can probably point to a better video, but here are a couple for Ion Torrent: http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=W3jPTBU9vF8 http://www.youtube.com/watch?v=yVf2295JqUg http://www.youtube.com/watch?v=yVf2295JqUg ...and the Nature paper: http://www.nature.com/nature/journal/v475/n7356/full/nature10242.html http://www.nature.com/nature/journal/v475/n7356/full/nature1... 1. http://dhruvbird.com/genome_compression.pdf http://dhruvbird.com/genome_compression.pdf