Blobtools view is used to generate a blobDB.table.json before creating a plot using blobtools plot.

Input

• a json file - output file created with Blobtools create.

Parameters

• taxrule - Taxrule used for computing taxonomy (supported: "bestsum", "bestsumorder") [ default: bestsum ]
• rank - Taxonomic rank(s) at which output will be written. (supported: 'species', 'genus', 'family', 'order', 'phylum', 'superkingdom', 'all') [default: phylum]
• hits - Displays taxonomic hits from tax files that contributed to the taxonomy.
• concoct - Generate cov files [default: False]
• calculate_cov - Legacy coverage when getting coverage from BAM file

Command line example:

• blobtools view -i prefix.blobDB.json

Output

• prefix.blobDB.table.json - a text base output file
• coverage file - a text base coverage file output file with column # contig_id read_cov base_cov # - if cov is specified
• prefix.blobDB.concoct_coverage_info.tsv - a text base coverage output file with base cov column only - if concoct is specified.

Contributor

Galaxy Australia wrapped the Blobtools: the original software is available in this Github repository.

References