Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism

TL;DR

Rawsamble enables direct de novo assembly from raw nanopore signals using a hash-based overlap detection, significantly speeding up the process and reducing memory without relying on basecalling or reference genomes.

Contribution

It introduces the first method for all-vs-all raw signal overlap detection and de novo assembly directly from nanopore signals, bypassing basecalling.

Findings

Provides 5x to 23x speedup over traditional pipelines.

Reduces peak memory usage by up to 22x.

Produces accurate unitigs up to half a chromosome in length.

Abstract

Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals directly if a reference genome is unknown due to a lack of accurate mechanisms to handle increased noise in pairwise raw signal comparison. Our goal is to enable the direct analysis of raw signals without a reference genome. To this end, we propose Rawsamble, the first mechanism that can identify regions of similarity between all raw signal pairs, known as all-vs-all overlapping, using a hash-based search mechanism. We use these overlaps to construct de novo assembly graphs with an existing assembler, miniasm, off-the-shelf. To our knowledge, these are the first de novo assemblies ever constructed directly from raw signals without basecalling. Our extensive evaluations across multiple genomes of varying sizes show that Rawsamble provides a significant speedup (on average by 5.01x and up to 23.10x) and reduces peak memory usage (on average by 5.74x and up to by 22.00x) compared to a conventional genome assembly pipeline using the state-of-the-art tools for basecalling (Dorado's fastest mode) and overlapping (minimap2) on a CPU.We find that around one-third of Rawsamble 's overlapping pairs are also found by minimap2. We find that when we use overlapping reads from Rawsamble, we can construct unitigs that are 1) as accurate as those built from minimap2's overlaps and 2) up to half a chromosome in length (e.g., 2.3 million bases for E. coli). Source code: https://github.com/CMU-SAFARI/RawHash