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)


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 The full benchmarking pipeline can be found at, while the benchmarking input FASTQ and output files can be found at

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


  • bacterial chromosome
  • genetics
  • plasmid


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