Plasmid Sequence Analysis from Long Reads v2

This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence. For plasmid sample preparation for nanopore sequencing, see here. The most recent version of our rapid barcoding kit protocol at the time this protocol was written is attached below: At the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads. Input(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST). I've noticed that the default demultiplexing carried out by Guppy and Dorado has some issues with chimeric reads, which can affect assembly. Output(s): Consensus sequence per barcode as a fasta file