Giulio Ermanno Pibiri

icon indicating a website link https://jermp.github.io icon indicating an email [email protected]

icon company Ca' Foscari University of Venice icon location Padova, Italy icon location Associate Professor of Computer Science. Focus on data structures, data compression, and code optimization.

Results 84 comments of Giulio Ermanno Pibiri

Support larger alphabets and k via generic kmer_t

Thanks. I'll try it myself later and see what happens. Perhaps is just the --eulertigs flag?

Support larger alphabets and k via generic kmer_t

Beautiful, thanks Oleksandr!

Support larger alphabets and k via generic kmer_t

Hi @adamant-pwn, sorry for the late reply. I do not think there are further actions :) SSHash on such larger k is so nice and powerful! If you're interested (and...

Support larger alphabets and k via generic kmer_t

Hi @adamant-pwn, sorry you're absolutely right! What I merged yesterday into the master branch was something I began earlier and that I wanted to make the default but just delayed...

Support larger alphabets and k via generic kmer_t

Fantastic! Thank you so much. I'll be running some benchmarks soon and keep you posted here. So, what's the largest kmer length we could use in your opinion and still...

Support larger alphabets and k via generic kmer_t

> For the largest kmer length, it's hard to tell because we didn't really try anything beyong k=127 yet. For me, k=127 seemed reasonably fast, but I don't know if...

How to get the most random randstrobes in compiled languages?

A little update on what I proposed: it is `h(k_1) ^ h(k')` , i.e., the XOR between the two hash codes, not just the hash of the XOR between the...

first attempt at vectorizing window.cpp

Hi @slice4e and thank you for this. However, you should test this first, at least, before submitting the PR :) Can you try it?

Vectorization

Sure, thank you for the suggestion! Are you willing to submit a PR with the vectorized code?

different runs return different number of unitigs and distinct color subsets

I'm CCing also @jnalanko who might be interested. Have you also notice this? I can confirm that different runs of themisto may report different number of color sets, e.g., 4,236,355...