MpGAP
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fmalmeida
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
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.
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 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.