obikmer

obikmer is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.

Constraints

• Target scale: individual genome datasets, tens of Gbases
• Maximum efficiency in computation, memory, and disk usage
• Input formats: FASTA, FASTQ, gzip, streaming stdin

Priority operations

• Kmer counting (frequencies)
• Fast search / query
• Set operations: union, intersection, difference