Stacks 2.0 Released: Major Update to Population Genomics Software
We’re excited to announce the release of Stacks 2.0, a major update to our population genomics software pipeline that’s been five years in development.
What’s New in Stacks 2.0
Improved Core Algorithm
- New assembly algorithm with better handling of polymorphic sites
- Reduced false positive SNP calls by 40%
- Faster processing - up to 3x speed improvement
- Better memory management for large datasets
New Features
- Population module: Integrated population genetics statistics
- Genetic mapping: Support for linkage map construction
- Paired-end support: Full integration of paired-end RAD data
- Plotting tools: Automated visualization of results
User Experience
- Simplified parameter selection
- Improved documentation and tutorials
- Docker container for easy installation
- Cloud computing support
By the Numbers
Since its initial release in 2013, Stacks has: - Been cited in over 3,000 publications - Processed data from 500+ species - Been downloaded 50,000+ times - Enabled population genomics in non-model organisms worldwide
Community Contributions
Stacks 2.0 includes contributions from users worldwide: - Bug reports and feature requests from hundreds of users - Code contributions from 15 external developers - Beta testing by 50+ research groups - Translations into 5 languages
Training Opportunities
We’re offering workshops on Stacks 2.0: - PAG 2019 (San Diego, January) - Evolution 2019 (Providence, June) - Online workshop (March, registration required)
Looking Forward
Development continues with planned features: - Machine learning for parameter optimization - Integration with genome assembly tools - Enhanced visualization capabilities - Support for long-read sequencing data
Download: catchenlab.life.illinois.edu/stacks
Documentation: Full manual and tutorials
Support: Google Group
Thanks to NSF and NIH for funding support, and to the thousands of users whose feedback has shaped this software.