Outputs

plassembler will output a _plasmids.fasta file, which will contain the assembled plasmid sequence(s) in FASTA format (including long and short read copy numbers in the header), and a _plasmids.gfa file, which will contain the assembly graph from Unicycler that can be visualised in Bandage.

plassembler also outputs a _summary.tsv file, which gives the estimated copy number for each plasmid, for both short reads and long reads (see this paper for more details about plasmid copy numbers) and also gives each contig's top hit by mash distance in the PLSDB (if there is a hit), along with all its supporting information.

If plassembler fails to assemble any plasmids at all in _plasmids.fasta, all these files will still exist, but will be empty (to ensure plassembler can be easily integrated into workflow managers like Snakemake).

plassembler will also output a log file, a flye_output directory, which contains the output from Flye (it may be useful to decide whether you need more sequencing reads, or some strange assembly artifact occured) and a unicycler_output directory containing the output from Unicycler. If --use_raven is specified, a raven_output director will exist instead of flye_output.

Other Outputs

If you use the --keep_fastqs flag, plassembler will keep FASTQ files containing all reads that went into the Unicycler assembly. These will be kept in the plasmid_fastqs directory. It will also keep all long reads that map to more than one contig as multimap_long.fastq.

If you use --keep_chromosome, Plassembler will keep the unpolished chromosome(s) as chromosome.fasta.

What happens if plassembler fails to find a plasmid?

• There are two reasons why plassembler will fail to find a plasmid:

• Where Flye assembles a complete chromosome, and then Plassembler fails to find any plasmids using the short reads. Most of the time, this simply means that there are no plasmids in the your bacterial isolate. Plassembler will still make output files (to ensure you can easily use it with workflow managers like Snakemake), but these will be empty.

• Where there is insufficient coverage for Flye to assemble a complete circular chromosome. In these cases, it is recommended that you either do more long read sequencing so that you can assemble a complete circular chromosome, or check that your -c parameter is correcting set.