John Lees

> Would you recommend an earlier PopPunk version for my analysis since the existing database must have been created using an earlier version? I guess my worry is whether version...

The second issue – ah I would have expected that to work. Yes you could try with update-db, or just add the column manually

Max k=63 as that's the largest we can fit in `u128`, which is the longest base type in rust. It is possible to add longer precision but this would be...

I actually think that SKA1 may work with any k-mer length so you could try that. Would still be interested to know why you want/need this

Ok interesting, thanks for sharing this. Unfortunately we don't have the capacity to add this at the moment, but I'll leave this issue open – if lots of people want...

1. Yep @rderelle is right here, mismatches is the proportion of split k-mers mismatching. Distance is number of SNPs distant (which could be normalised by genome or alignment length. If...

You'll definitely need to fix the reads issue before a comparison can be made. In each of your ska fastq commands: ``` ska fastq NYC112574_urmc_cdiff_1/NYC112574_urmc_cdiff_1_1.fastq.gz NYC112574_urmc_cdiff_1/NYC112574_urmc_cdiff_1_2.fastq.gz -o NYC112574_urmc_cdiff_1 ``` This...

Thanks @ktmeaton for the detailed explanation, reproducible example, and likely fix -- this is all really really helpful! Strictly, p-values have different interpretations with different N, so dropping some values...

I'm guessing max_pi is coming out wrong. Can you add `print(max_pi)` to above line 257 and rerun?

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