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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

PLoS computational biology, 2017-06, Vol.13 (6), p.e1005595-e1005595 [Peer Reviewed Journal]

COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6): e1005595. https://doi.org/10.1371/journal.pcbi.1005595 ;2017 Wick et al 2017 Wick et al ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6): e1005595. https://doi.org/10.1371/journal.pcbi.1005595 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005595 ;PMID: 28594827

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Title:
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Author: Wick, Ryan R ; Judd, Louise M ; Gorrie, Claire L ; Holt, Kathryn E
Phillippy, Adam M.
Subjects: Accuracy ; Algorithms ; Assemblies ; Assembling ; Assembly ; Bacteria ; Biochemistry ; Bioinformatics ; Biology and Life Sciences ; Biotechnology ; Chromosome Mapping - methods ; Cloning ; Construction costs ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Drug resistance ; E coli ; Gene sequencing ; Genome, Bacterial - genetics ; Genomes ; High-Throughput Nucleotide Sequencing - methods ; Medicine and Health Sciences ; Methods ; Molecular biology ; Nucleotide sequencing ; Porosity ; Research and Analysis Methods ; Resolution ; Science ; Sequence Alignment - methods ; Sequence Analysis, DNA - methods ; Software ; User-Computer Interface
Is Part Of: PLoS computational biology, 2017-06, Vol.13 (6), p.e1005595-e1005595
Description: The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate "hybrid" assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler.
Publisher: United States: Public Library of Science
Language: English
Identifier: ISSN: 1553-7358
ISSN: 1553-734X
EISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1005595
PMID: 28594827
Source: Geneva Foundation Free Medical Journals at publisher websites
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

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