摘要：SummaryThird-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and potentially gap-free assemblies. The larger effective length of their reads has provided a means to overcome the challenges of short to mid-range repeats. Currently, accurate long read assemblers are computationally expensive, whereas faster methods are not as accurate. Moreover, despite recent advances in third-generation sequencing, researchers still tend to generate accurate short reads for many of the analysis tasks. Here, we present HASLR, a hybrid assembler that uses error-prone long reads together with high-quality short reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on most of the samples, while being on par with other assemblers in terms of contiguity and accuracy.Graphical AbstractDisplay OmittedHighlights•We introduce HASLR, a fast tool for hybrid assembly of short reads and long reads•HASLR proposes a new data structure called backbone graph•The backbone graph provides a large-scale map of the whole genome•Our experiments demonstrate that HASLR generates low number of misassembliesGenomics; Bioinformatics; Sequence Analysis
