Matthew DeMaere

URL to biorxiv doesn't point to your manuscript.

1

Did you want the URL to take people to the top page at biorxiv rather than your manuscript?

Reference data necessary for Braken.

3

For your extension of the GTDB, it would be great if you could provide the full Kraken folder from which to build a Braken database. i.e. from Braken's documentation >...

Why is the installed Python library different depending on build method? Re: bioconda

4

I'll start this off by saying I want to get the Jellyfish Python bindings into the Jellyfish bioconda package. If I can't get this to work, I'll either have to...

Memory allocation error due to large hash leaves behind orphaned generator processes

1

- Jelllyfish 2.3.0 - Clean install of Ubuntu 18.04 LTS - gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0 **Situation** When counting kmers and requesting a hash size that is larger than available memory,...

I realize this is a very old repository, but I might as well pass back these minor changes.

Refactoring of main loop

1

Based off @papanikos earlier fork, this pull request goes further to refactor the main loop. Filtering of sequence length is now possible for short and long sequences, as I found...

Article supplementary data is unavailable.

4

I've tried to obtain the supplementary data from your article published with Oxford Bioinformatics, but there is a problem with the site and no URL is provided. Are you able...

Updated bcalm calls to reflect UX changes, but not sure where or if bglue exists.

Annotations for community definitions

1

Currently, many simulation options are an all-or-nothing operation that affect the entire community. Adding these are annotations within the community definition would provide valuable fine-grained control. ## Example Simulations that...

Community profile format is cumbersome

1

The format used to define a community is presently a simple flat table. This approach incurs a great deal of duplicated information, and a cleaner approach would be a to...