OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

Summary: Tumor xenograft sequencing libraries inevitably contain infiltrating murine host reads, but conventional deconvolution tools fail on bisulfite sequencing (BS-seq) because chemical C-to-T deamination collapses sequence entropy and destroys graft recall (< 0.015%). We present OTTER, an automated, compiled multi-omics workflow framework that decouples execution into static domain operators, an immutable reference registry, and a native strand-aware edit-distance engine, restoring bisulfite deconvolution (52%-54% recall across a 0%-99% compositional gradient) while preserving complete decision parity on transcriptomics. Availability and implementation: OTTER is implemented in Go and Rust, runs on x86_64 Linux (including CentOS 7 with glibc 2.17), and is freely available open-source under the MIT License at https://github.com/otterlab-bio/otter; test and validation data are provided at https://huggingface.co/datasets/fallingstar10/otter-data.