Asaph enables analysis of large inversions from SNP data. Asaph employs streaming and dimensionality reduction to be fast and maintain a small memory footprint. Asaph is developed primarily by RJ Nowling and students at MSOE.
Tutorials describing how to use Asaph and associated resources are located in the tutorials directory.
- Installing Asaph
- Preparing, Importing, and PCA of SNPs
- Detecting and Localizing Inversions
- Genotyping Inversions
Other tutorials related to Asaph:
- Testing Changes to Asaph (mostly for developers)
- Preparing the Inversion Benchmark Data Set (optional, only if you don't have your own data)
Asaph and associated methods have been described in the following papers:
- RJ Nowling, F Fallas-Moya, et al. Fast, low-memory detection and localization of large, polymorphic inversions from SNPs. PeerJ 2022.
- RJ Nowling, KR Manke, and SJ Emrich. Detecting inversions with PCA in the presence of population structure. PLOS One 2020.
- RJ Nowling and SJ Emrich. Detecting Chromosomal Inversions from Dense SNPs by Combining PCA and Association Tests. Proceedings of the 9th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB 2018), August 2018.
- RJ Nowling and SJ Emrich. Adjusted Likelihood-Ratio Test for Variants with Unknown Genotypes. Journal of Bioinformatics and Computational Biology (JBCB), 16(5) 2018.
