COBS (COmpact Bit-sliced Signature index) 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 and the false positive rate of the index determined at construction time. COBS' compact but simple data structure outperforms 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.
More information about COBS is presented in our research paper: Timo Bingmann, Phelim Bradley, Florian Gauger, and Zamin Iqbal. COBS: a Compact Bit-Sliced Signature Index arXiv:1905.09624, May 2019.
COBS requires CMake, a C++17 compiler or the Boost.Filesystem library.
To download and install COBS run:
git clone --recursive https://github.com/bingmann/cobs.git
mkdir cobs/build
cd cobs/build
cmake ..
make -j4
and optionally run make test to check the build.
COBS can read FASTA files (*.fa, *.fasta, *.fa.gz, *.fasta.gz), FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz), McCortex files (*.ctx), or text files (*.txt).
You can either recursively scan a directory for all files matching any of these files, or pass a *.list file which lists all paths COBS should index.
To check the document list to be indexed, run for example
src/cobs doc-list tests/data/fasta/
To construct a compact COBS index from these seven example documents run
src/cobs compact-construct tests/data/fasta/ example.cobs_compact
Check --help for many options.
Maybe the most important is --canonicalize to enable k-mer DNA canonicalization.
COBS has a simple command line query tool:
src/cobs query -i example.cobs_compact CTDNIETFYCTNSYRYENVPRPIYVWVLFQEDEWHGYR
or a fasta file of queries with
src/cobs query -i example.cobs_compact -f query.fa
In our paper we compare COBS against seven other k-mer indexing software packages. These are the main results, scaling by number of documents in the index, and in the second diagram shown per document.