After a long time, I am proud to present the first stable release of Jam, my new genomic minhashing tool. Jam emphasizes performance and accuracy, and it aims to make searching for "small" sequences, such as plasmids, phages, and mobile elements, more efficient in "large" genomic sets, such as metagenomes.
What's Changed
- Added jamhash dependency, benchmark jamhash improve jamhash performance, in-depth analysis compared to murmur3
- Removed LMDB support, added new custom storage format
- Removed GC / Length tracking, added full bias table support using Count-min-sketches
- Added fast pre-filter using state-of-the-art BinaryFuseFilters
- Heavily optimized performance, reduced IO and memory load.
- Added mmap support for .jam files
- Added .bias files for pre-computed bias tables
- Added shannon-entropy low complexity filtering
Full Changelog: v0.1.0-beta.2...v0.9.10