OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow
- 1Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, China
Abstract
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.
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BibTeX
@misc{zheng2026otter,
title = {{OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow}},
author = {Y. Zheng and X. Liu and Y. Yi and X. Sun and F. Liu and X. Yan and C.-H. Man and H. Gu and X. Wang and F. Zhang},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.24.761506},
url = {https://www.biorxiv.org/content/10.64898/2026.10.24.761506v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow
AU - Y. Zheng
AU - X. Liu
AU - Y. Yi
AU - X. Sun
AU - F. Liu
AU - X. Yan
AU - C.-H. Man
AU - H. Gu
AU - X. Wang
AU - F. Zhang
PY - 2026
DA - 2026/10/24
PB - bioRxiv
DO - 10.64898/2026.10.24.761506
UR - https://www.biorxiv.org/content/10.64898/2026.10.24.761506v1
AB - 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.
ER -