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@etvedte etvedte released this 15 Dec 16:13
· 19 commits to main since this release
v0.5.0
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Learn about vigilant mode.

  • Added option to use prosplign instead of miniprot to align proteins as annotation evidence

    • Prosplign is most likely to help in organisms with less RNA-seq, and/or those that are more distant from other genomes with protein sets
    • Prosplign is more computationally expensive than miniprot

  • Added new protein sets with many more species and protein selection logic

    • User-specified number of taxa to use from a protein set, selecting the taxonomically-closest
    • Can exclude protein sets by taxid
    • Can supplement default sets with user-provided proteins

  • Added tRNA feature annotation using tRNAscan

  • Added rRNA feature annotation using Rfam

  • Added other short ncRNA feature annotation (with the exception of miRNAs) using cmsearch

  • Revisions to ortholog reference names to better meet GenBank standards

  • Improvements for plant gene naming

  • Adjust CPU settings for some tasks (e.g. STAR) to improve efficiency

  • Reduce footprint of EGAPx working directories

  • Fixed an issue where minimap2 fails by renaming long reads #166

  • Fixed an issue where BUSCO wasn't producing output in some situations

  • Fixed an issue where EGAPx failed when sequence titles are absent in genome FASTA files #173

  • Fixed an issue where EGAPx failed when run with no RNA-seq

  • Fixed an issue where EGAPx was downloading extra SRA runs

  • Added asn_adjust to image, which can be used to edit ASN in some situations

  • Improvements to prepare_submission for GenBank submission:

    • annotation provider can be specified GP-40924
    • handling for multispecies BioProjects
    • outputs final GFF3 file which can incorporate adjustments to structural/functional annotation

  • Documentation updates

    • Added documentation for new features
    • Added documentation for recommended genome FASTA formatting
    • Updated documentation for recommended RNAseq formatting
    • Clarified EGAPx does not annotate organelles
    • Added language about prepare_submission errors that can be ignored
    • Added EGAPx diagram
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