- butter and maple (the old aligner and MIRNA finder) are no longer required. ShortStack 3 contains both the aligner and MIRNA finding capabilities.
- Improved alignment algorithms for multi-mapped reads -- better speed and better precision.
- Vastly improved performance on highly fragmented genome assemblies via 'genome stitching' (making artificial larger contigs from many small ones).
- Support for the newer CRAM alignment format, as well as BAM
- Simplified usage
Download it from github and see the test data to get started. We are working on a manuscript describing the novel and highly improved alignment methods that ShortStack 3.0 uses to place multi-mapped small RNA reads in the most likely originating position.