Question: Does jellyfish 2 support kmer size > 31
2
gravatar for Chen
2.3 years ago by
Chen890
Chen890 wrote:

In Jellyfish's original paper(Marcais et al, Bioinformatics 2011), it says that "counting kmers up to 31 bases in length".

But on the other hand, in other papers such as KMC2 (Deorowicz et al, Bioinformatics 2015), Jellyfish2 is used to count kmer size = 55.

So does Jellyfish support k > 31 now? and How it is supported?(i.e. why in original version it is not supported but now it is supported)?

Thanks.

kmer counting kmer jellyfish • 965 views
ADD COMMENTlink modified 2.2 years ago • written 2.3 years ago by Chen890
4
gravatar for John
2.3 years ago by
John12k
Germany
John12k wrote:

Probably because they originally used 64bits per kmer, which can store up to 32 bases in 2bit (less one for whatever reason, probably to signal reverse complementation or variable-lengths).

With an update, this man-made constraint was removed.

ADD COMMENTlink written 2.3 years ago by John12k

Thanks again for your kind help.

ADD REPLYlink written 2.2 years ago by Chen890
3
gravatar for Chen
2.2 years ago by
Chen890
Chen890 wrote:

I will answer this question by myself.

I did some test on kmers greater than 31, and at least for the test dataset, the current version of jellyfish does support kmer length > 31.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Chen890

As you suggested I cleaned up the thread, please edit your answer to include that you also dived in the code to confirm this. (That part got lost by deleting comments.)
Most of us are really friendly, occasionally sarcastic. So you can always assume the best intentions ;-)

ADD REPLYlink written 2.2 years ago by WouterDeCoster40k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1155 users visited in the last hour