Does jellyfish 2 support kmer size > 31
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4.8 years ago
Chen ★ 1.1k

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.

jellyfish kmer kmer counting Jellyfish • 1.7k views
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4.8 years ago
John 13k

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.

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Thanks again for your kind help.

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4.8 years ago
Chen ★ 1.1k

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.

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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 ;-)

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