Plassembler: an automated bacterial plasmid assembly tool

Bioinformatics. 2023 Jul 1;39(7):btad409. doi: 10.1093/bioinformatics/btad409.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Benchmarking
  • High-Throughput Nucleotide Sequencing* / methods
  • Plasmids / genetics
  • Sequence Analysis, DNA / methods
  • Software*