Felipe Marques de Almeida
Felipe Marques de Almeida
To facilitate contribution and updates, would be great to create github actions to test the pipeline with the available profiles and technologies.
Add in the pipeline a rule so all the assemblies of a sample have a copy stored in a single folder, e.g. `final_output`, so that it is easier for users...
Unicycler has now made a huge [release to v0.5.0](https://github.com/rrwick/Unicycler/releases/tag/v0.5.0). So, it would be nice to have the pipeline now using this version. For that, a few fixes in the pipeline's...
Pilon is the tool used for polishing long reads assemblies in the pipeline. It would be nice to also add [polypolish](https://github.com/rrwick/Polypolish) tools as the second short-reads polisher for long reads...
Add option to use Pacbio hifi in assemblers were an option for it is available, such as Canu, Flye and etc.
A new tool for long reads quality assessment is now available: * https://github.com/yfukasawa/LongQC The task is to evaluate the tool and compare it with NanoPack and pycoQC in order to...
Consider changing the software used to filter the long reads in order to use a more recent and faster app. Currently, [NanoFilt](https://github.com/wdecoster/nanofilt) is used for the task. The software to...
Close #247 Close #313 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code...
During #118 it was detected an issue in the `INTEGRON FINDER` tool. We opened an issue in the tool's repo, https://github.com/gem-pasteur/Integron_Finder/issues/114 Once the fix is available on a new release,...
**Background** This issue is meant to address the comments received on the paper review [here](https://f1000research.com/articles/12-1205/v1#referee-response-219643). **Description** Update the provided bacterial-analysis Zenodo dataset so that it also contains the example outputs...