RT Journal Article
SR Electronic
T1 HASLR: Fast Hybrid Assembly of Long Reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.01.27.921817
DO 10.1101/2020.01.27.921817
A1 Ehsan Haghshenas
A1 Hossein Asghari
A1 Jens Stoye
A1 Cedric Chauve
A1 Faraz Hach
YR 2020
UL http://biorxiv.org/content/early/2020/01/28/2020.01.27.921817.abstract
AB 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.