For reference, Jellyfish is supposed to be state of the art for fast
k-mer counting
http://www.cbcb.umd.edu/software/jellyfish/
Kasper
On Thu, Feb 7, 2013 at 6:51 PM, Hervé Pagès wrote:
> Hi Dario,
>
>
> On 02/05/2013 05:00 PM, Dario Strbenac wrote:
>>
>> Hello,
>>
>> Would it be possible to i
Hi Dario,
On 02/05/2013 05:00 PM, Dario Strbenac wrote:
Hello,
Would it be possible to include an option that firstly goes through all of the
strings and runs a sliding window along them, to find all the unique k-mers
present in the dataset ?
Finding the unique k-mers in the dataset can eas
Hello,
Would it be possible to include an option that firstly goes through all of the
strings and runs a sliding window along them, to find all the unique k-mers
present in the dataset ? This would avoid having a sparse matrix with many
columns of all zero counts, when a larger value of width i
