Jamshed Khan

Hello @Krannich479, glad to know your interest in using cuttlefish (and thanks for attending the DSB'21 talk)! The functionalities that you proposed to include looks great. We certainly have these...

Hi @kevyin, thank you for using cuttlefish! We'll need some more information to look into this. Would it be possible for you to provide the reference data that you had...

Hi @marekkokot: mentioning a related update! Recently we released cuttlefish [v2.2.0](https://github.com/COMBINE-lab/cuttlefish/releases/tag/v2.2.0), which builds and runs on M1 and M2. For such, we (@TheJasonFan) patched KMC to adopt [SIMDe](https://github.com/simd-everywhere/simde), and this...

Hi @rob-p and @Daniel-Liu-c0deb0t , The proposed encoding here is a nice one. Albeit, the A = 0, C = 1, G = 2, and T = 3 encoding does...

Hi @rob-p, Sure, obviously we can define the canonical k-mer with self-consistency under any bijective mapping from the nucleotide-bases to integers. My point is that *if* defining the canonicalization function...

Hello Moustafa, We do not support this at this moment, unfortunately. It _might_ be doable, given that we have the corresponding KMC databases; but attaching the _k_-mer counts to the...

Hi @shokrof: are you using cuttlefish 2, i.e. using the `--read` or `--ref` arguments? If yes, then we have valid counts only for the (_k_ + 1)-mers—the _k_-mers are extracted...

@rob-p: should it be build-able now?

Hi @deyuanyang: Thank you for using cuttlefish! I see that you're using FASTQ inputs---in that case, you need to pass the `--read` argument. Besides, I also see that you're using...

Hello @shenweima, Thank you for using cuttlefish! Could you please detail your use-cases a bit more? That way, we might be able to help you better. Regards.