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Ecogenomics / GTDBNCBI

The GTDB provides the software infrastructure for working with a large collection of genomic resources. The major goal of this initiative is to provide a phylogenetically consistent taxonomy for archaea and bacteria.
https://gtdb.ecogenomic.org/
GNU General Public License v3.0
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Representative genomes should never be filtered #42

Closed donovan-h-parks closed 8 years ago

donovan-h-parks commented 8 years ago

The selection criteria for GTDB representatives is becoming increasingly complex. As such, some representatives actually have relatively poor CheckM quality estimates. Such genomes may represent known reduced genomes or genomes present as a single ungapped chromosome which are almost certainly complete (though may not pass the strict quality thresholds).

Selected representatives should NEVER be filtered out of the GTDB trees. These are considered trusted genomes. If the user request representatives they should always get the complete set.

pchaumeil commented 8 years ago

This has been has been implemented and will be available in the next release of GTDB.