With recent developments in sequencing technologies, it is now conceivable to combine a long-read-first assembly method with short-read polishing to quickly and cheaply produce full bacterial chromosomal assemblies that are nearly flawless. However, current techniques for assembling bacterial plasmids from long-read-first assemblies sometimes assemble incorrectly or even completely miss bacterial plasmids, necessitating manual curation. A tool called Plassembler was created to automatically assemble and produce bacterial plasmids using a hybrid assembly method. By deleting chromosomal reads from the input read sets via a mapping approach, it improves accuracy and computing efficiency in comparison to the current gold standard tool Unicycler.
‘conda install -c bioconda plassembler’ can be used to install plassembler, which is a bioconda package that is implemented in Python. The source code can be found at https://github.com/gbouras13/plassembler, where it is accessible. The benchmarking input FASTQ and output files can be accessed at https://doi.org/10.5281/zenodo.7996690, and the complete benchmarking pipeline is available at:
https://github.com/gbouras13/plassembler_simulation_benchmarking.
Reference:
Bouras G. et. al.(2023) Plassembler: an automated bacterial plasmid assembly tool. Bioinformatics 39(7): btad 409