BlobToolKit is a software suite that helps researchers identify and isolate non-target data in genome assemblies. It allows for interactive exploration of assembly, read, and analysis files in a browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. The software uses GC proportion and coverage as major axes to display contigs or scaffolds and overlays taxonomic assignments to help separate signals from noise. It also includes taxonomic attribution based on sequence similarity searches using BLAST and Diamond. BlobToolKit can be used to separate contigs and scaffolds into bins for subsequent reanalyses and to provide quality assurance for publicly released genome assemblies. The software is used in conjunction with the European Nucleotide Archive (ENA) to enhance understanding and utility of submitted data. BlobToolKit is available as a public instance at https://blobtoolkit.genomehubs.org/view. The software includes a variety of visualizations, including blob plots, cumulative plots, snail plots, and BUSCO scores, which allow for the identification of contaminants and cobionts. BlobToolKit is also used in the analysis of publicly available genome assemblies, including those from the ENA. The software is freely available under open source licenses and includes a Docker image for easy deployment. BlobToolKit has been used to analyze a variety of genome assemblies, including those from the Drosophila albomicans and Conus consors assemblies, highlighting the importance of identifying contaminants and cobionts in genome assemblies. The software has also been used to identify mis-annotated records in public databases, such as those from the thicket tinamou genome assembly. BlobToolKit is a significant extension of the approach launched in BlobTools, allowing for user interaction with the rich data associated with each contig in the Viewer mode. The software is used in three main ways: in the research laboratory to sequence the genome of a new species, in the publication and visualization of published assemblies, and in comparative and evolutionary genomics. BlobToolKit provides a powerful tool for identifying contaminants and cobionts in genome assemblies and enhancing the credibility of genome assemblies.BlobToolKit is a software suite that helps researchers identify and isolate non-target data in genome assemblies. It allows for interactive exploration of assembly, read, and analysis files in a browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. The software uses GC proportion and coverage as major axes to display contigs or scaffolds and overlays taxonomic assignments to help separate signals from noise. It also includes taxonomic attribution based on sequence similarity searches using BLAST and Diamond. BlobToolKit can be used to separate contigs and scaffolds into bins for subsequent reanalyses and to provide quality assurance for publicly released genome assemblies. The software is used in conjunction with the European Nucleotide Archive (ENA) to enhance understanding and utility of submitted data. BlobToolKit is available as a public instance at https://blobtoolkit.genomehubs.org/view. The software includes a variety of visualizations, including blob plots, cumulative plots, snail plots, and BUSCO scores, which allow for the identification of contaminants and cobionts. BlobToolKit is also used in the analysis of publicly available genome assemblies, including those from the ENA. The software is freely available under open source licenses and includes a Docker image for easy deployment. BlobToolKit has been used to analyze a variety of genome assemblies, including those from the Drosophila albomicans and Conus consors assemblies, highlighting the importance of identifying contaminants and cobionts in genome assemblies. The software has also been used to identify mis-annotated records in public databases, such as those from the thicket tinamou genome assembly. BlobToolKit is a significant extension of the approach launched in BlobTools, allowing for user interaction with the rich data associated with each contig in the Viewer mode. The software is used in three main ways: in the research laboratory to sequence the genome of a new species, in the publication and visualization of published assemblies, and in comparative and evolutionary genomics. BlobToolKit provides a powerful tool for identifying contaminants and cobionts in genome assemblies and enhancing the credibility of genome assemblies.