pirovc

Thank you @jtembrockhaus , well done! Just one minor comment and once solved I will merge the PR into the dev branch.

Thanks for reporting. Indeed they changed a while ago. A PR would be great! You have to update the [urls](https://github.com/pirovc/multitax/blob/396e19c1c9dfdfb13b9ea673ed8b34fd5ce3873b/multitax/ncbitx.py#L28) and the parsing procedure, the `download_files` function should be generalized...

I just run the same command here and it works fine. `ncbi_tx = NcbiTx()` downloads the NCBI taxdump file and my guess is that you probably had some network issues...

Hi Peter, you can try [using the `--filter-type ibf`](https://pirovc.github.io/ganon/default_databases/#filter-type-ibf-and-hibf) and maybe [change the `--mode`](https://pirovc.github.io/ganon/default_databases/#fixed-size-and-mode-only-for-filter-type-ibf) to get smaller databases and use less RAM. However, using default HIBF is recommended due to...

> Right now I have all sequences in a single file. It looks like the build step creates about 200k symlinks to the same file in `viruses_files/build`. So it would...

Just a heads-up, a new ganon version (2.0) is planned to be out soon(ish) and there will be some parameter changes, where `--hibf` will vanish since it will be the...

ganon2 (ganon v2.0.0) is now released. The new behavior is to generate the `.hibf` by default with `ganon build` and `ganon build-custom`. The option to switch to the old filter...

Thanks for sharing the code @mortonjt . I would also be interested on the implementation of VLR

Thanks for sharing @jolespin, looks like you already did it all so integration should be straightforward and jugding by this issue, proportionality would be a good fit for scikit-bio. @mortonjt...

@jolespin do you plan to create the PR? If not I start it and we work there together. I already sketched the functions based on code posted previously here, the...