HASLR: Fast Hybrid Assembly of Long Reads

Abstract

Third generation sequencing technologies from platforms such as Oxford Nanopore Technologies and Pacific Biosciences have paved the way for building more contiguous assemblies and complete reconstruction of genomes. The larger effective length of the reads generated with these technologies has provided a mean to overcome the challenges of short to mid-range repeats. Currently, accurate long read assemblers are computationally expensive while faster methods are not as accurate. Therefore, there is still an unmet need for tools that are both fast and accurate for reconstructing small and large genomes. Despite the recent advances in third generation sequencing, researchers tend to generate second generation reads for many of the analysis tasks. Here, we present HASLR, a hybrid assembler which uses both second and third generation sequencing 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 all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

Population genetic structure of the carrot weevil (Listronotus oregonensis) in North America

“…First, the long‐read assembly pipeline wtdbg2 (v2.5; Ruan & Li, 2020) was used to generate an initial set of contigs using the parameter –X 25, ‐x preset1, ‐g 1.3G, ‐L 8k, ‐p 21, ‐‐edge‐min 2, and ‐‐rescue‐low‐cov‐edges set. In a second assembly, the short reads were combined with a 25× subset of the longest nanopore reads using the hybrid assembler HASLR (v.0.8a1; Haghshenas et al, 2020) under default settings. Both assemblies were then merged into a single draft using Quickmerge (v.0.3; Chakraborty et al, 2016).…”

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

“…New software and technology versions are frequently released, thus making comparisons obsolete within months. There are efforts to optimise assemblers towards speed and reduced memory usage (Gatter et al, 2021;Haghshenas et al, 2020;Shafin et al, 2020). While this is important to complete extremely large plant genome assemblies and to reduce the environmental impact of bioinformatics, quality improvements are still of interest and would be beneficial for smaller genomes.…”

A Deep Dive into Genome Assemblies of Non-vertebrate Animals

“…Canu, MECAT, MECAT2, NECAT and NextDenovo correct low-accuracy long reads prior to assembly; Flye, Raven and NextDenovo have a polishing step; and many assemblers include a scaffolding step to yield both contigs and scaffolds. Some assemblers propose a hybrid assembly strategy, using both short and long reads, such as HALSR [246], MaSuRCA [247] and WENGAN [248].…”