A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler's hybrid assemblies.

"all sequence data generated in this study (illumina and ont raw read data genome assemblies) have been deposited under ncbi bioproject accessions prjna886432 and prjna1010135 and biosample accessions samn37105267 ( bacillus thuringiensis subsp tenebrionis strain ten bi 256-82/cm3) and samn37179813 ( bacillus wiedmannii strain eps29)."

"all underlying code of the galaxy workflow is available at https://github com/wennj/plasmid-collapse-gene-loss-unicycler-galaxy .; the r script which was used to create figs4 and s1 is available in the online version of this article (supplementary material 1). the r script which was used to create figs4 and s1 is available in the online version of this article (supplementary material 1)."

"Conflicts of interest The authors declare that there are no conflicts of interest."

"Funding information This study received funding from JKI Project BioSam."