COBS: a Compact Bit-Sliced Signature Index

Abstract: We present COBS, a COmpact Bit-sliced Signature index, which is a cross-over between an inverted index and Bloom filters. Our target application is to index $k$-mers of DNA samples or $q$-grams from text documents and process approximate pattern matching queries on the corpus with a user-chosen coverage threshold. Query results may contain a number of false positives which decreases exponentially with the query length. We compare COBS to seven other index software packages on 100000 microbial DNA samples. COBS' compact but simple data structure outperforms the other indexes in construction time and query performance with Mantis by Pandey et al. in second place. However, unlike Mantis and other previous work, COBS does not need the complete index in RAM and is thus designed to scale to larger document sets.