Curtis dev - Githubissues

kapsakcj / nanoporeWorkflow

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

MIT License

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Curtis dev #5

Closed kapsakcj closed 4 years ago

kapsakcj commented 5 years ago

big ole PR that adds:

updates and changes to Guppy-on-GPU script 01_basecall-w-gpu.sh
downsampling/filtering of reads using filtlong via singularity to highest quality 600Mb of reads >1kb
assembly of downsampled/filtered reads using flye 2.5 via singularity
4X racon polishing of flye draft assembly
medaka polishing of racon-polished assembly via singularity
updated readme's with new content and clarity

Removed:

qcat from 01_basecall-w-gpu.sh since Guppy does demultiplexing/trimming

Takes care of #4