Learn how to use BlobTools2 by following these tutorials. (If you’re here while they are still being written, take a look at the original Getting Started with BlobTools2 page for some example commands.)
To run the commands you will either need to use the BlobToolKit Docker image or follow the instructions to install BlobToolkit.
Creating a dataset
The minimum requirement to create a new dataset with BlobTools2 is an assembly FASTA file, but it is possible to create a much richer dataset by adding additional data and metadata. The underlying BlobDir data structure makes it trivial to separate dataset creation from the subsequent addition of analyses (see Adding data to a dataset) and presents the data in a format that can be efficiently processed for interactive visualisation. Read more…
Adding data to a dataset
Once you have a BlobDir dataset (see Creating a dataset), further data can be added by parsing analysis output files into one or more fields using the blobtools add command. Dedicated parsers are available for a range of analysis types, assigning values to each contig in an assembly: BLAST or Diamond hits provide taxonomic assignments; read mapping files provide base and read coverage; BUSCO results show completeness metrics for full and filtered assemblies; and fields from generic text files can be imported for maximum flexibility. Read more…
Updating metadata
Dataset metadata, including links to external resources, can be added or updated using the blobtools add command. Read more…
Filtering a dataset
Coming soon. Read more…
Opening a dataset in the viewer
Coming soon. Read more…
Generating plots on the command line
Coming soon. Read more…