I am on my way back from ASMCUE! It was a fun adventure. As I wait for my flight back to RDU, I was able to watch the Nanopore Learning course on Human genome sequencing and analysis and the video on “Introduction to data generation and sequencing output for analysis.” The presenter presented about the five steps of the Oxford Nanopore Technologies analytical workflow:
- Raw data acquisition – real-time basecalling
- QC
- Primary data analysis (alignment or classification)
- Secondary data analysis (assembly, variant calling, expression)
- Analysis completion
Live and local analysis is done with MinKNOW integrated analysis. If reads cannot be basecalled (“skipped”), “catch-up” time will be necessary. Stand alone analyses can be done with Guppy. Cloud options such as EPI2ME provide options for demultiplexing, 16S, WIMP, and ARMA workflows. MinKNOW produces basecalled fast5 and fastq files. The speaker noted that there are several resources on the Nanopore Community and Github pages. This video may be older, as I think ONT is moving away from the use of Guppy. Nevertheless, the workflow graphic and comparison of live and post-run basecalling options was useful.
