Two overall categories exists for taxa for which genome quality exceptions can be requested under the SeqCode.
The first case entails genomes for which it is believed that the quality estimates are incorrectly estimated in the contributor checks and/or the automated estimates. In this case, the onus is on the contributor/s to provide sufficient evidence for how the quality checks fail and why it is believed that the estimates are incorrect. This could entail showing systematic reductions in genome size across a particular lineage when estimates for completeness are consistently low, or showing the consistent presence of marker genes in multiple copies in multiples genomes of a taxon that leads to inflated contamination estimates, or other approaches that show how or why the estimates are considered to be incorrect. In this case, it is strongly recommended that this evidence is included in a publication, as a means of documenting this in literature. A brief description of this evidence should also be included in the "submitter comments" section of the genome submission form, which will become publicly visible if validated. These exceptions are granted at the discretion of the SeqCode genomics curators and/or may be discussed among the SeqCode Registry and Nomenclature Working Group depending on the case.
The second case entails genomes for which the quality estimates are believed to be correct, and the genome quality falls under the SeqCode genome quality requirements. In these cases, a formal request for exception should be submitted to the SeqCode Reconciliation Commission and the reasons for this exceptions need to be effectively communicated. This formal request for decision and community discussion should follow the format established for the discussion on Omnitrophus fodinae (https://github.com/seq-code/seqcode/discussions/2) and should be submitted through GitHub Discussions. We will then notify the secretary of the SeqCode Reconciliation Commission. Following discussion among the Reconciliation Commission, and a three month public discussion period, the Reconciliation Commission will vote on whether the exception can be granted, and the Executive Board will be notified of the decision. A public announcement will then follow on the decision. Here, the exceptions are granted by majority vote of the Reconciliation Commission.
For additional information on the structure and members of the different parts of the SeqCode Committee, see https://seqco.de/committee