Hi Dan, I've been following this issue for a while - the good news (see other threads on this BAI limitation) is the replacement Coordinate Sorted Index (CSI) from Heng Li which is implemented in htslib (now used internally by samtools) fixes this limitation.
Which is good news for plant geneticists, people working on certain marsupials, and any other organisms with long chromosomes. Regards, Peter On Wed, Jul 23, 2014 at 10:58 AM, Dan Bolser <[email protected]> wrote: > Interesting thread! > > I like these comments: > "This is twice as long as the longest human chromosome and is > quite adequate for practical use" - Thomas W. Blackwell > "Hopefully 2 Gbp suffices for most species that people are > interested in." - John Marshall. > > As already mentioned, bread wheat, which provides ~20% of all the > calories consumed by humans globally, has 6 of it's 27 chromosomes > *assembled* to a length of greater than 537 Mbp [1]... > > I won't mention Paris japonica ;-) > > > [1] > https://docs.google.com/spreadsheet/ccc?key=0Aqs5UFlky_s6dDlmVVFib3FoSm1tS1JIQzMxY0RVb2c ------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
