Can Geneious Prime assemble PacBio or Minion data?

PacBio sequencers produce two types of data.  PacBio CCS (Circular Consensus Sequence) data is reasonably good quality and we recommend this for assembly in Geneious Prime.  The Map to Reference algorithm in Geneious handles these reads reasonably well, but for de novo assembly we recommend changing the advanced setting "Maximum Gap Size" to at least 5.  Geneious R10 and later contains improvements that produce better results with PacBio CCS data.  

PacBio CLR (Continuous Long Read), and similarly Oxford Nanopore Minion data, has longer reads but much lower quality.  Because of the high error rate, these reads cannot be reliably assembled using the Geneious assembler. However, different data sets tend to vary greatly in quality to the point where some data sets are quite usable for map to reference yet other data sets have quality so low that they are unusable with the Geneious assembler.  

Plugins for assembling PacBio and Oxford Nanopore data are available for Geneious Prime 2020 onwards.  Minimap2 (available for Prime 2020.0+) is a popular reference mapper recommended for noisy long read data.  Flye (available for Prime 2020.1+) is a de novo assembler for single molecule sequencing reads.  

For hybrid assemblies of PacBio or Nanopore data with Illumina data we recommend using SPAdes, see this post for details.  

Note that Geneious cannot import Minion fast5 format.  You can convert fast5 to fastq using Poretools (see http://poretools.readthedocs.org/en/latest/).  Converted fastq data can then be imported into Geneious. 

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