MinION Gadgets - A bioinformatic toolbox

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(1) Basecalling

High accurarcy basecalling with Guppy. Execute ClusterBasecalling.sh on the Cluster. You need to modify the parameters in the first rows of the script

(2) NanoPlot

Run NanoPlot analysis of the BaseCalled reads, or subsets of it. The information to be passed to the script Nanoplot.sh needs to be provided in a sequencing_summary.txt as generated by the Guppy pipeline. A typical commandline looks like this:

sh shell/Nanoplot.sh \
path/to/sequencing_summary.txt \
path/to/outputfolder \
SomeName

(2) Lambda reads

This pipeline isolates reads with BLAST hits against the lambda phage reference J02459.1 with an e-value < 1e-100 and produces a NanoPlot summary for this subset (see above).

sh shell/Lambda.sh \
path/to/InputfolderWithAllFastqFiles \
path/to/outputfolder \
path/to/sequencing_summary.txt