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# sketches
[](https://pkg.go.dev/github.com/shenwei356/bio/sketches)
This package provides iterators for k-mer and k-mer sketches
([Minimizer](https://academic.oup.com/bioinformatics/article/20/18/3363/202143),
[Scaled MinHash](https://f1000research.com/articles/8-1006),
[Closed Syncmers](https://peerj.com/articles/10805/)).
K-mers are either encoded (k<=32) or hashed (arbitrary k, using [ntHash](https://github.com/will-rowe/nthash)) into `uint64`.
Related projects:
- [kmers](https://github.com/shenwei356/kmers) provides manipulations for bit-packed k-mers (k<=32, encoded in `uint64`).
- [kmcp](https://github.com/shenwei356/kmcp) uses this package.
## Benchmark
CPU: AMD Ryzen 7 2700X Eight-Core Processor, 3.7 GHz
$ go test . -bench=Bench* -benchmem \
| grep Bench \
| perl -pe 's/\s\s+/\t/g' \
| csvtk cut -Ht -f 1,3-5 \
| csvtk add-header -t -n test,time,memory,allocs \
| csvtk pretty -t -r
test time memory allocs
------------------------------------------ ------------ -------- -----------
BenchmarkKmerIterator/1.00_KB-16 11445 ns/op 0 B/op 0 allocs/op
BenchmarkHashIterator/1.00_KB-16 7974 ns/op 24 B/op 1 allocs/op
BenchmarkSimHashIterator/1.00_KB-16 79477 ns/op 48 B/op 1 allocs/op
BenchmarkProteinIterator/1.00_KB-16 17852 ns/op 432 B/op 2 allocs/op
BenchmarkMinimizerSketch/1.00_KB-16 56071 ns/op 48 B/op 2 allocs/op
BenchmarkSyncmerSketch/1.00_KB-16 101310 ns/op 977 B/op 7 allocs/op
BenchmarkProteinMinimizerSketch/1.00_KB-16 29914 ns/op 736 B/op 5 allocs/op
## History
This package was originally maintained in [unikmer](https://github.com/shenwei356/unikmer).
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