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HASLR: Fast Hybrid Assembly of Long Reads

Resource type
Date created
2020-08-21
Authors/Contributors
Author: Stoye, Jens
Author: Hach, Faraz
Abstract
Third-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 formany 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.
Document
Identifier
DOI: 10.1016/j.isci.2020.101389
Published as
Haghshenas, E., Asghari, H., Stoye, J., Chauve, C., & Hach, F. (2020). HASLR: Fast Hybrid Assembly of Long Reads. IScience, 23(8), 101389. https://doi.org/10.1016/j.isci.2020.101389.
Publication title
IScience
Document title
HASLR: Fast Hybrid Assembly of Long Reads
Date
2020
Volume
23
Issue
8
Copyright statement
Copyright is held by the author(s).
Scholarly level
Peer reviewed?
Yes
Language
English
Member of collection
Download file Size
PIIS2589004220305770.pdf 2.81 MB

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