Vladimir Mikryukov

Dear Taylor! Thank you so much for the valuable comments and corrections! I will modify my PR accordingly soon (probably after the Nextflow Summit). Considering the database parameter, I think...

Sourmash module PR from Taylor Reiter: https://github.com/nf-core/modules/pull/2176 (not merged yet)

For taxonomy profiling, we need a new module `sourmash/gather` (https://github.com/nf-core/modules/issues/2214)

`sourmash/gather` should be working now (https://github.com/nf-core/modules/pull/2250). Now it's the turn for the `sourmash/taxonomy` module.

Hello! I'm heavily engaged with my day job at the moment and unfortunately, I can't dedicate the necessary time to this project now. I apologize for any inconvenience caused by...

> auxiliary scripts are missing from path, although they are in the environment Theses scripts are in `opt` directory (e.g., `~/miniconda3/opt/clark/`, if the software was installed in the base environment)....

Example code to build the database: ``` ~/miniconda3/opt/clark/set_targets.sh DB fungi --genus ~/miniconda3/opt/clark/set_targets.sh DB2 bacteria --species ```

@Midnighter That's correct, Metaxa2 uses rRNA only. It identifies rRNA in metagenomic shotgun data using HMM-profiles (could be considered as a database, but it should be more sensitive, as it...

As far as I know, authors build HMMs from the curated sequence alignments (SSU and LSU, independent for different tax groups). It is very similar to `ITSx` tool (used in...

Hello Ming, Thank you for reporting the issue. I've fixed the problem (closed via 5e9c680). Please pull the latest version of `metagMisc`. It works on a test dataset: ``` library(phyloseq)...