Felipe Marques de Almeida

Assess possibility of adding the https://github.com/HIT-ImmunologyLab/DBSCAN-SWA#usage tool

For now the generated circos plot is very limited. It should be enhanced with: - [ ] Possibility to add genes of different tools instead of only `AMRFinderPlus` and `VFDB`...

Assess the possibility of using new [ICEO](https://github.com/ontoice/ICEO) from ICEberg database to scan and annotate ICEs in a more consistent manner instead of using BLAST alignments and filters. It may improve...

Assess what is required and how to implement some nice features performed in https://github.com/gbouras13/hybracter such as the coupled polishing of polypolish+pypolca which seem to work nicely in a complementary manner....

Now that `hifiasm` was included in the pipeline, it must assessed how the pipeline can be adapted in order to allow the user to pass on hi-c and/or parental data...

Include a way to automatically download data from SRA and run the pipeline. Bottleneck here is identifying a way so that the pipeline can fetch multiple SRAs for a single...

add 3 hybrid strategy

1

Add another hybrid strategy for samples where this might be the best option. This strategy is to perform a short reads assembly and then scaffold with long reads.

Add trycycler tool to generate a consensus assembly of long reads tools as an option.

Check if there are new version available of tools and update it.

Assess and consider the change from 'porechop' which is deprecated to porechop_abi which is under maintenance. https://github.com/bonsai-team/Porechop_ABI