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Mapping-Assisted Targeted-Assembly for Metagenomics
If no reads are re-mapping on a scaffold after keeping only the best equivalent reads alignments, we have to output a warning. This behavior has to be followed up. This...
When I try to run matam_assembly.py from the conda installation MATAM, I get an error that it doesn't recognize an option `--perform_taxonomic_assignment`. Does conda version not include this option?
One way to add a user guide to this project could be to add GitHub Pages
This would need validation on our test datasets that we dont loose any relevant information (ex: we drop low abundance species). We should also count how many scaffolds were dropped...
Right now, the `-d` option has a different usage in `index_default_ssu_rrna_db.py` + `matam_db_preprocessing.py` vs. `matam_assembly.py`. In the first case, the user has to provide the path to a directory where...
Pros: - GitLab is fully open-source - the repository can be hosted on the main GitLab server or on a private server - exact same functionalities as GitHub + additional...
RDP assign confidence scores at each level of the taxonomic hierarchy. For the moment this information is lost during the transformation to KRONA representation.
Today, we just know if an error happened during a MATAM run, and at which step. Moreover, a MATAM run can keep on going even if there was a major...
* Clustered db: #sequences & mean_length & min_length & max_length * Complete db: #sequences & mean_length & min_length & max_length
Currently, the tool used to cluster the database is Vsearch. It will be interesting to also provide sumaclust. Sumaclust: * Pro: Slightly better results * Cons: Slow Vsearch * Pro:...
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Mapping-Assisted Targeted-Assembly for Metagenomics