Supported Data FilesLong read data (PacBio and Oxford Nanopore Technologies) data can be processed as FASTA files. Two predefined Procedure Details can be used when importing files manually or in a pipeline. Currently the pipelines (e.g., SMRT Link for PacBio or Chopper, Flye, and Medaka for ONT) of the vendors must be used for base-calling, assembly, polishing, and circularization. Optional the topology and coverage information can be extracted from the contigs of the FASTA files if stated as following:
Thereby, also a NCBI conform naming of the contigs can be achieved; e.g., for a circular chromosome: Using in the pipeline a tool like Circlator to fixstart (and orientation) helps tremendously for downstream visualization and comparisons of chromosomes and plasmids. For chromosomes Circlator uses for this function by default matches to the dnaA gene. For defining the start and orientation of most plasmids the CGE PlasmidFinder replicon database that is used for rep-typing could be utilized. Importing Run InfoPacBio run infos can be imported. |