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Further Assessment of Genome Annotation #75

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GallVp opened this issue Aug 13, 2023 · 2 comments · Fixed by #89
Closed

Further Assessment of Genome Annotation #75

GallVp opened this issue Aug 13, 2023 · 2 comments · Fixed by #89
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done on dev The issue has been resolved by development on the 'dev' branch
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2.0.0

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GallVp commented Aug 13, 2023

From: https://www.biorxiv.org/content/10.1101/2022.10.03.510643v3

  1. The mono-exonic (single-exon) and multi-exonic (multiple exon) ratio
  2. Conserved single-copy orthologs queried from the predicted gene models using BUSCO
  3. Gene prediction assessment with EnTAP v0.10.8 (Hart et 19 al., 2020) using a 70% reciprocal functional annotation approach with NCBI’s Refseq Plant and 20 Uniprot databases.
@GallVp GallVp added the v2 label Aug 13, 2023
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GallVp commented Aug 13, 2023

Code is already available here: https://gitlab.com/PlantGenomicsLab/easel

@GallVp GallVp removed the v2 label Apr 16, 2024
@GallVp GallVp added this to the 2.0.0 milestone May 3, 2024
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GallVp commented May 3, 2024

  1. is already there.
    BUSCO should be added.
  2. requires annotation and should be part of a genome annotation pipeline.

@GallVp GallVp self-assigned this May 3, 2024
@GallVp GallVp added the done on dev The issue has been resolved by development on the 'dev' branch label May 22, 2024
@GallVp GallVp mentioned this issue May 30, 2024
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@GallVp GallVp closed this as completed in #89 Jun 5, 2024
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Candidate for 2.0.0 Plant-Food-Research-Open/assemblyqc
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