This dataset contains a fasta file and its Bowtie2 index. The fasta file includes publicly available genomes of 5 termite species, namely Zootermopsis nevadensis (Terrapon, N., Li, C., Robertson, H. M., Ji, L., Meng, X., Booth, W., ... & Liebig, J. (2014). Molecular traces of alternative social organization in a termite genome. Nature communications, 5(1), 1-12.), Cryptotermes secundus (Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., ... & Bornberg-Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature ecology & evolution, 2(3), 557-566.), Macrotermes natalensis (Poulsen, M., Hu, H., Li, C., Chen, Z., Xu, L., Otani, S., ... & Zhang, G. (2014). Complementary symbiont contributions to plant decomposition in a fungus-farming termite. Proceedings of the National Academy of Sciences, 111(40), 14500-14505.), Coptotermes formosanus (Draft genome sequence of the termite, Coptotermes formosanus: Genetic insights into the pyruvate dehydrogenase complex of the termite) and Reticulitermes speratus (Shigenobu, S., Hayashi, Y., Watanabe, D., Tokuda, G., Hojo, M. Y., Toga, K., Saiki, R., Yaguchi, H., Masuoka, Y., Suzuki, R., Suzuki, S., Kimura, M., Matsunami, M., Sugime, Y., Oguchi, K., Niimi, T., Gotoh, H., Hojo, M. K., Miyazaki, S., … Maekawa, K. (2022). Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. Proceedings of the National Academy of Sciences, 119(3), e2110361119.). These genomic sequences have been classified with Kraken 2 v2.1.2 (Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 1–13 and Wood, D. E., & Salzberg, S. L. (2014). Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biology, 15(3).) to remove all microbial sequences. This cleaned fasta file was indexed using the bowtie2-build command from Bowtie2 (Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357–359.) and can be used to perform alignments.