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Introduction to live basecalling in MinKNOW
For MinION Mk1B, Flongle on MinION Mk1B, and PromethION 2 Solo, the MinKNOW software presents an option to basecall reads on the local computer. The basecalling is carried out live, as the read files are generated during a sequencing experiment.
Basecalling results are displayed in real-time in the MinKNOW user interface, and data is written out in the BAM or FASTQ file format.
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Live alignment in MinKNOW
Basecalled reads can be aligned to a reference during the sequencing run. To do this, you will need to upload a reference FASTA or .mmi file during run set-up, and optionally a BED file when there is a specific interest in a particular region of the reference (e.g. specific gene in a chromosome).
A reference file can contain multiple entries in the same file (e.g. multiple chromosomes), and alignment hits from these files are used to populate the alignment graphs which can be viewed on the MinKNOW UI. Alignment hits from BED files will appear in the sequencing .txt file generated in the data folder.