cambiotraining/sars-cov-2-genomics

pipeline cheatsheet

Opened this issue · 1 comments

tavareshugo commented

Write a cheatsheet page that summarises the steps for generating the consensus assembly.

Maybe this could be written as a sort of protocol:

  • Before you start:
    • type of data (nanopore or illumina)
    • artic primer version used
    • nanopore: pore, device name, caller version (for medaka models)
    • check software and nextflow config files
  • Steps:
    • commands to run the pipeline
    • downstream analysis examples (e.g. phylogenies)
tavareshugo commented

this can also serve as a template worksheet for a shorter in-person training