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Plant-Food-Research-Open / assemblyqc

A Nextflow pipeline for evaluating assembly quality
https://plant-food-research-open.github.io/assemblyqc/
MIT License
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Further Assessment of Genome Annotation #75

Closed GallVp closed 4 months ago

GallVp commented 1 year ago

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 commented 1 year ago

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

GallVp commented 5 months ago
  1. is already there. BUSCO should be added.
  2. requires annotation and should be part of a genome annotation pipeline.