Reproducibility archive for "SynDe: Syndrome-guided Decoding of Raw Nanopore Reads"

This repository contains the experimental data, simulation scripts, and results necessary to reproduce the results of the paper "SynDe: Syndrome-guided Decoding of Raw Nanopore Reads". We propose two algorithms: PrimerSeeker, which efficiently detects primer sequences in raw nanopore sequencing reads, and SynDe, a decoder that operates on the same raw reads and supports any linear error correction code with a low-complexity graphical representation. The simulation scripts call our implementations of PrimerSeeker and SynDe, the source code for which can be found here and here. A summary of our results can be found in the Jupyter notebooks in analysis-jupyter-notebooks/. The FAST5 files used in our simulations are obtained from the datasets published by Volkel et al. (10.5281/zenodo.11985454), Xu et al. (10.5281/zenodo.7995806), and Lau et al. (https://github.com/shubhamchandak94/nanopore_dna_storage_data/tree/bonito), and are included here for reproducibility. This record contains the same content as our GitHub repository, with the addition of large files (files in `fast5_datasets`, `alignments` and `basecall`) excluded from GitHub due to file size constraints.