The Geneious assembler can handle data from Sanger and high-throughput (NGS) sequence platforms. Because diﬀerent sequencing platforms have diﬀerent error proﬁles and rates, they may require diﬀerent assembly parameters. To ensure the optimal parameters are used for your dataset you can set the sequencing platform under Sequence → Set Read Technology. This can also be set during the ﬁle import process if you are importing fastq ﬁles.
The Geneious assembler works well with Sanger, Illumina, Ion Torrent, 454, and PacBio CCS data. PacBio CLR and Oxford Nanopore data are more problematic for Geneious due to the very high error rates. Depending on the data quality, you may be able to use these with map to reference, but are unlikely to be able to successfully de novo assemble them. When de novo assembling only Illumina sequencing data, turning oﬀ ’Allow gaps’ (in the advanced options) can sometimes improve performance and results. If any of the input sequences are set as PacBio or Oxford Nanopore, Geneious will automatically use a maximum gap size of 2 to 3 times the speciﬁed value.
Both the Geneious de novo assembler and mapper will also work with arbitrarily long reads. For example, you can use high quality contig consensus sequences as input to either of these.