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Tanya Berardini

Tanya Berardini

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  1. Assembly
    1. need to work out details of tracking the metadata on BioSample provenance for the individual pieces
    1. K. Schneebeger's group's work on assembling a Col-Community Consensus (CC) assembly is likely to finish by the end of 2022, and will incorporate C. Pikaard's group's data on NOR2 and NOR4, 4 Col-0 MA lines from F. Rabanal/D. Weigel
    2. Col-CC should be submitted to NCBI as an independent assembly
    3. Idea to visualize the multiple individual assemblies that were combined to make Col-CC as a patchwork (GCV? other visualization tool?)
  2. Automated Annotation
    1. NCBI will take the Col-CC assembly when accepted by NCBI and available and will run it through their eukaryotic annotation pipeline
    2. need to resolve details on whether or not to include the Araport11 proteins as evidence
    3. add isoSeq from PRJNA755474 from this paper to next run
    4. please send more recent isoSeq/RNA-seq/CAGE experimental data in GenBank to include in the next run
  3. Manual Review
    1. TAIR to investigate hosting requirements/existing training tools, ease of output of information needed for NCBI submission even before manual review begins
    2. used by many MODs to maintain their genomes, concurrent editing possible, community maintained code
    1. TAIR as coordinator
    2. Klass van Wijk: anything to do with proteins (including small peptides - sORFs, etc) and protein isoforms (AS, etc)
    3. Kai Ye : We (XJTU team) would work on centromeres and microsatellite sites.
    4. Shujun Ou, Alex Bousios: TEs, ATHILAs
    5. Craig Pikaard: NOR2 and NOR4, rDNAs
    1. WebApollo as tool
    2. Community experts
  4. Submission to NCBI/GenBank
    1. begin working on release early, no need to wait till manual review is done, can be done with dummy data to work out format issues
  5. Dissemination
    1. broad support for authorship on V12 paper for ALL who were involved in effort, in any stage of the process
    2. V12 release to be incorporated into TAIR, BAR, etc as soon as possible after NCBI RefSeq is updated to this version

Action items

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    We'll check in by email in mid-December to get an update from Korbinian and from TAIR on the assembly progress and WebApollo.