Initial publication release for Xenomorph v1.0.0. Models available for B, S, P, Z, X, K, J, V detection on ONT r9.4.1 flowcells.
Xenomorph is a suite of tools used for nanopore sequencing of alternative 'xeno'-basepairs (XNAs). This toolkit incorporates ONT-workflows to preprocess FAST5 files and extract signal levels for kmers in a sequence. Models parameterized on XNA basepairs can then be used to test if signal levels match XNA pairs. Xenomorph relies on kmer models that were parameterized using libraries of XNA-containing DNA. The general pipeline consists of two steps: 1) preprocessing FAST5 reads and extracting level information and 2) basecalling using a selected kmer model. This version of Xenomorph was built and tested on Oxford Nanopore Technologies r.9.4.1 flow cells (Flongle or MinION). Xenomorph will continue development and updating models to track the latest releases of Nanopore chemistry.
This public repository is maintained by the XenoBiology Research Group at the University of Washington, Department of Chemical Engineering.
Future releases will support signal segmentation using ONT Remora api and models for r10.4.1 flowcells. See existing branches for more information.