Benchmarking datasets for deluxpore: a demultiplexing Nextflow pipeline for Illumina dual-indexed Nanopore libraries

This dataset contains the benchmarking data and results supporting the findings for deluxpore, a Nextflow pipeline designed to demultiplex Nanopore reads from Illumina dual-indexed libraries (NEBNext and Nextera). Contents of the compressed file (deluxpore_benchmarking_data.tar.gz):- randomize.sample2indexes.tsv: Experimental design file mapping samples to their respective i5 and i7 index pairs.- output_badread/: Demultiplexing results summaries for the 96-sample combinatorial design across quality thresholds (Q10, Q20, Q25, Q30).- output_badread.8samples/: Demultiplexing results summaries for the optimized 8-sample unique-index configuration.- randomize.reference/: Demultiplexing results summaries for the 96-sample combinatorial design for references sequences (sequences with no errors - perfect demultiplexing). This directory also contains raw initial reference sequences used as input for BadRead simulations (randomize.reference/randomize.reference_seqs.fastq.gz). Methodology:Read errors were simulated using BadRead to model realistic Nanopore error rates and positional variability from 1500nt long reference sequences. Demultiplexing was performed using deluxpore v1.0. The data summaries present in this repository were used to generate Figure 1 and Supplementary Figures in the associated manuscript. Related Software:- Source code: https://github.com/compgenomicslab/deluxpore- Benchmarking scripts: https://github.com/compgenomicslab/deluxpore-benchmarking