• Plassembler: an automated bact...

Treffer: Plassembler: an automated bacterial plasmid assembly tool.

Title:
Plassembler: an automated bacterial plasmid assembly tool.
Authors:
Bouras G; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.; The Department of Surgery - Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network, Adelaide, South Australia 5000, Australia., Sheppard AE; School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia., Mallawaarachchi V; Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, South Australia 5042, Australia., Vreugde S; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.; The Department of Surgery - Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network, Adelaide, South Australia 5000, Australia.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2023 Jul 01; Vol. 39 (7).
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
High-Throughput Nucleotide Sequencing*/methods , Software*, Sequence Analysis, DNA/methods ; Plasmids/genetics
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Entry Date(s):
Date Created: 20230627 Date Completed: 20230710 Latest Revision: 20250106
Update Code:
20250114
PubMed Central ID:
PMC10326302
DOI:
10.1093/bioinformatics/btad409
PMID:
37369026
Database:
MEDLINE

Weitere Informationen

Summary: With recent advances in sequencing technologies, it is now possible to obtain near-perfect complete bacterial chromosome assemblies cheaply and efficiently by combining a long-read-first assembly approach with short-read polishing. However, existing methods for assembling bacterial plasmids from long-read-first assemblies often misassemble or even miss bacterial plasmids entirely and accordingly require manual curation. Plassembler was developed to provide a tool that automatically assembles and outputs bacterial plasmids using a hybrid assembly approach. It achieves increased accuracy and computational efficiency compared to the existing gold standard tool Unicycler by removing chromosomal reads from the input read sets using a mapping approach.
Availability and Implementation: Plassembler is implemented in Python and is installable as a bioconda package using 'conda install -c bioconda plassembler'. The source code is available on GitHub at https://github.com/gbouras13/plassembler. The full benchmarking pipeline can be found at https://github.com/gbouras13/plassembler_simulation_benchmarking, while the benchmarking input FASTQ and output files can be found at https://doi.org/10.5281/zenodo.7996690.
(© The Author(s) 2023. Published by Oxford University Press.)