A simple CLI and module for k-mer analysis

Before you begin...

The K-mer database profile kmerdb is a file format (.kdb) and command-line utility (CLI) for creating k-mer count vector profiles from sequencing data. kmerdb views k-mers and their De Bruijn graphs as fundamental tools for biological sequence abundances and sequence similarities. K-mer methods have been noted as fast and are used in areas from NGS quality control to phylogenomic investigations.

kmerdb is based on the block GNU-zip file (bgzf) standard. Each .kdb file has a metadata header section, much like .bam files. It is essentially a tab-delimited format with a YAML header. Input file checksums, unique and total k-mer counts, and nullomer 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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