Adding BUSCO

Adding BUSCO data to a dataset allows BUSCO scores to be shown for the full dataset and recalculated for filtered datasets. Files for multiple lineages can be imported for comparison.

Example

Example BUSCO files for Strongyloides venezuelensis can be obtained from the BlobToolKit downloads site:

cd ~/BTK_TUTORIAL/FILES

curl http://blobtoolkit.genomehubs.org/download/ALIAS/S_v/S_venezuelensis_HH1/S_venezuelensis_HH1.busco.nematoda_odb9.tsv.gz | gunzip -c > ASSEMBLY_NAME.busco.nematoda_odb9.tsv

curl http://blobtoolkit.genomehubs.org/download/ALIAS/S_v/S_venezuelensis_HH1/S_venezuelensis_HH1.busco.metazoa_odb9.tsv.gz | gunzip -c > ASSEMBLY_NAME.busco.metazoa_odb9.tsv

These files can be imported to add BUSCO annotations to the assembly contigs:

~/blobtoolkit/blobtools2/blobtools add \
    --busco ~/BTK_TUTORIAL/FILES/ASSEMBLY_NAME.busco.nematoda_odb9.tsv \
    --busco ~/BTK_TUTORIAL/FILES/ASSEMBLY_NAME.busco.metazoa_odb9.tsv \
    ~/BTK_TUTORIAL/DATASETS/ASSEMBLY_NAME

Configuration

There are 2 configuration options when adding BUSCO results using blobtools add:

  • --busco – BUSCO full summary file to import. [Required]
  • --replace – Replace existing fields if present. [Default: false]

--busco

One or more BUSCO full_summary TSV files can be specified using the --busco flag. The files will be added to the dataset in the order they are specified, with the first file used to show BUSCO scores in the BlobToolKit Viewer snail view.

Usage:

blobtools add \
    --busco ASSEMBLY_NAME.busco.nematoda_odb9.full_summary.tsv \
    --busco ASSEMBLY_NAME.busco.metazoa_odb9.full_summary.tsv \
    --busco ASSEMBLY_NAME.busco.eukaryota_odb9.full_summary.tsv \
    ...

--replace

If a blobtools add command would overwrite an existing field, the default behaviour is to issue a warning and not replace the existing field. To change this behaviour and allow existing fields to be overwritten, set the --replace flag.

Usage:

blobtools add \
    ...
    --replace \ 
    ...