add Racon and Flye scripts...

kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers

MIT License

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add Racon and Flye scripts... #4

Closed kapsakcj closed 5 years ago

kapsakcj commented 5 years ago

Also write wrapper script so once Guppy-GPU basecalling is done, script runs qcat-->Flye-->Racon X4 --> Medaka

Also maybe add filtlong in there too?

kapsakcj commented 5 years ago

No longer using qcat, since latest release of Guppy v3.2.2 now demultiplexes and trims barcodes. Flye and Racon modules added. Still need to adjust medaka script to take the output assembly of Racon