Datasets can be filtered based on the values in any variable (e.g. GC proportion and length) or category field (e.g. assigned phylum), or by using a list of identifiers (sequence IDs). Filters may be applied to a complete dataset to allow for use of a reduced dataset without repeating analyses or applied to assembly FASTA and read FASTQ files to allow for reassembly and reanalysis. Filter parameters are all shared between BlobTools2 and the BlobToolKit Viewer, allowing interactive sessions to be reproduced on the command line.