Eric Coissac
461 B
461 B
obikmer
obikmer is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.
Constraints
- Target scale: metagenomic data, tens of Gbases, billions of kmers
- 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