Introducing BlobToolKit

BlobToolKit is an open-source collection of analysis pipelines and interactive data exploration tools, designed to help identify, classify and filter contaminants and cobionts in genomic datasets.

We have begun running our analysis pipeline on all eukaryotic assemblies with INSDC accessions to formally assess the extent of contamination in the public databases and will continue to make these analyses available for exploration through an interactive viewer, e.g. Crassostrea gigas example dataset.

BlobToolKit follows on from the development of Blobology1 and BlobTools2 over the past few years in the Blaxter Lab at the University of Edinburgh. As development on BlobToolKit has only just begun, users interested in applying these approaches should continue to use Dom Laetsch’s BlobTools package directly until the methods are fully incorporated into BlobToolKit.

If you’d like to get in touch about any aspect of the project, please tweet us @blaxterlab or @rjchallis or email

Kumar et al. 2013. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Frontiers in Genetics, 4:237

Laetsch & Blaxter 2017. BlobTools: Interrogation of genome assemblies [version 1; referees: awaiting peer review]. F1000Research, 6:1287 (doi: 10.12688/f1000research.12232.1)