16 lines
461 B
Markdown
16 lines
461 B
Markdown
|
# 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
|