Plassembler: an automated bacterial plasmid assembly tool

George Bouras, Anna E. Sheppard, Vijini Mallawaarachchi, Sarah Vreugde

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)
61 Downloads (Pure)

Abstract

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.

Original languageEnglish
Article numberbtad409
Number of pages6
JournalBioinformatics
Volume39
Issue number7
DOIs
Publication statusPublished - Jul 2023

Keywords

  • bacterial chromosome
  • genetics
  • plasmid

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