Comments (4)
To this end, it needs:
- to find a way to install OBITools // or just replace obiuniq step with something else
- update CREST to CREST4 and thus support updated Silva and PR2 databases
- check RDPTools and staff how not to depend on local files
- remove CROP at all
edit if more will come
from pema.
A zenodo repo was built to host the classifiers pema uses along with the databases that have been trained with.
from pema.
Crest will not be upgraded for the time being.
Instead the files required for the case of PR2 and Silva 138
from pema.
Since pemabase:v.2.1.0
all precompiled dependencies for pema are on the zenodo repo already mentioned.
New databases wiil have to be added in those directories based on the current pemabase
architecture.
We ll consider about upgrading the CREST classifier in a future version.
This issue is now resolved.
from pema.
Related Issues (20)
- add remove_singletons option in OTU pipeline HOT 4
- Error when unzipping using a checkpoing HOT 1
- HPC job specifications HOT 4
- custom_ref_db doesn't work. HOT 5
- Upgrade to crest4
- provide pema main data product in a 7-level taxonomy format HOT 3
- extended final table HOT 1
- PEMA Ro-Crate HOT 1
- PEMA to create a run summary file HOT 2
- MIDORI updates HOT 2
- Unexpected Singletons in Final Table despite removeSingletons set to "Yes" HOT 5
- Error PEMA ASV inference: Directory swarm does not exists HOT 5
- 16s copy number
- When Swarm is chosen for the ITS, the names of the sequences are OtuXX and not ASVXX HOT 4
- Needed updates on "PEMA's output files.md" HOT 2
- time consuming preprocessing
- Storage usage of PEMA HOT 1
- pandaseq error "Something is wrong with this ID" HOT 17
- Long recurrent taxonomic labels HOT 1
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