We provide gapped k-mer indexes for the contamination removal tool Cleanifier. For human read removal, we provide two versions: One version uses a probabilistic Cuckoo filter (FPR $2^{-14}$, smaller, cleanifier_probabilistic.tar) and the other a bucketed Cuckoo hash table (exact, cleanifier_exact.tar); see https://doi.org/10.1093/bioinformatics/btaf632 for more details. For removal of ribosomal RNA from metatranscriptomic data, we provide an index (cleanifier_ribosomalRNA.tar) that contains all small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA available at the SILVA database (release 138.2). The software is available via GitLab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/) and Bioconda (https://anaconda.org/bioconda/cleanifier). The indices can be used with Cleanifier versions > 1.0.0.