ANNOTATION in the config file about comparative-annotation-toolkit HOT 3 OPEN

Hi -

Can you please explain what inputs you would be using for the CAT run?

The config [ANNOTATION] field is used to assign the reference genome against which you would like to annotate your other species. Currently, CAT supports using only one reference.

The hal file will have to be made using all the species you would like to annotate against the reference and the reference as well.

Please let me know if you need any further clarification.

Thanks!

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Hi,
I am reproducing the pangenome annotation in the A draft human pangenome reference article, and I wonder if I can add several GFF files of closely related species into the cat-hprc.gencode38.auto somes.config file to gain better gene annotate (these related species do not appear in the HAL file). Besides，should the chromosome names in the GFF files used in contig be consistent with those in the HAL file.

uigi --module cat RunCat --hal=CHM13-f1g-90-mc-aug11.hal --ref genome=GRCh38 --workers=8 --config=cat-hprc.gencode38.auto somes.config --work-dir work-hprc-gencode38-chm13 --out-dir out hprc-gencode38-chm13 --local-scheduler --assembly-hub --maxCores
8 --binary-mode local > cat.hprc.gencode38.autosomes.chm13.log

from comparative-annotation-toolkit.

from comparative-annotation-toolkit.