llk578496

[feature] Add option --nanohq in assembly when using bactopia with ONT reads

3

Hi @rpetit3 **Is this something you would like to see added?** It will be great to have the option `--nanohq` when performing de novo assembly in `bactopia`, just like you...

[question] Tutorial for having Nanopore reads only in Bactopia documentation

19

Hi @rpetit3 , Thank you so much for upgrading `Bactopia` to v2 which included supports for only Nanopore reads! We have been waiting for a very long time! May I...

**Related To** - [ ] Bactopia Tools - mlst **Is this something you would like to see added?** Would be great to have `Clonal Complex` included.

Tool Name: KmerFinder 3.2 Tool Link: KmerFinder Software - https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/ KmerFinder Database - https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/ KmerFinder Webserver - https://cge.cbs.dtu.dk/services/KmerFinder/ Available on [Bioconda](https://bioconda.github.io/)? no Available on [nf-core/modules](https://github.com/nf-core/modules)? no

[bactopia-tool] pMLST

3

Tool Name: pMLST Tool Link: Hosted by PubMLST - https://pubmlst.org/bigsdb?db=pubmlst_plasmid_seqdef Hosted by CGE - https://bitbucket.org/genomicepidemiology/pmlst/src/master/ Available on [Bioconda](https://bioconda.github.io/)? No Available on [nf-core/modules](https://github.com/nf-core/modules)? No

Tool Name: Mobile Element Finder Tool Link: Webserver - https://cge.cbs.dtu.dk/services/MobileElementFinder/ Mobile Element Finder Software - https://bitbucket.org/mhkj/mge_finder/src/master/ Mobile Element Finder Database - https://bitbucket.org/mhkj/mgedb/src/develop/ Available on [Bioconda](https://bioconda.github.io/)? No Available on [nf-core/modules](https://github.com/nf-core/modules)? No

[question] Nanopore only reads analysis skipped CALL_VARIANTS

7

Hi @rpetit3 We just tried to analyze only the Nanaopore reads, but seems it skipped the `CALL_VARIANTS` part. May I ask it is possible to include the `CALL_VARIANTS` analysis in...

[bactopia-tool] Add Phylophlan3.0.2 in Bactopia Tools

4

**Related To** - [ ] Bactopia Tools **Is this something you would like to see added?** [Phylophlan3.0.2](https://github.com/biobakery/phylophlan) does the phylogenetic analysis on prokaryotes based on core-protein, would like to see...

UnboundLocalError: local variable 'uniprotkb2uniref90' referenced before assignment

1

Hello @fasnicar We just tried to set up the database for _Burkholderia pseudomallei_, but we got the following error messages. **Error message:** `[e] unable convert UniProtKB ID to UniRef90 ID...

[feature] Full AMRFinderPlus search combining results to get maximum information

2

Hi @rpetit3 , **Related To** - [x] Bactopia - [x] Bactopia Tools **Is this related to a problem?** **Is this something you would like to see added?** It might be...