Pipeline for long-range PCR Nanopore data analysis

We developed and validated a Nanopore-based workflow for the analysis of heterogeneous long-range PCR (LR-PCR) amplicons targeting IS1071 composite transposons. Using an equimolar mixture of seven reference amplicons and environmental samples from a pesticide biopurification system, we benchmarked direct Nanopore sequencing against short-read DNBSEQ™ data. The pipeline integrates read clustering, read collapsing, and multi-step polishing aiming at consensus read generation. From Nanopore data, the pipeline recovered 15 high-quality consensus sequences (3.5–28 kb), all flanked by IS1071 tags.