Before you begin...

The K-mer database (.kdb) is a file format and command-line utility (CLI) for accessing precomputed k-mers from sequencing data. .kdb views k-mer graph databases as a fundamental technology to look at biological sequence identities and abundances. K-mer methods have been noted as fast and are used in areas from NGS quality control to phylogenomic investigations.

.kdb is based on the block GNU-zip file (bgzf) standard. Each .kdb file has a header or metadata section, much like .bam files. It is essentially a tab-delimited format with the last column unstructured for k-mer specific metadata. Input files and total k-mer counts are stored in the metadata block at the top of the file

Please visit the Install page for details on installation.

See the commands in the Usage section for an idea of what functionality is built in to kdb.

See the original blog post on the concept here.


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