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@dialvarezs dialvarezs released this 21 May 11:20
· 69 commits to main since this release
v1.0
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dialvarezs Diego Alvarez S.
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Learn about vigilant mode.

Initial version of the pipeline. Includes:

  • Basecalling and demultiplexing using ONT Guppy (optional, requires Guppy previously installed)
  • Assembly and variant calling using ARTIC
  • Variant annotation using SnpEff
  • Identification of clades/lineages of GISAID, Pangolin and Nexstrain
  • Quality metrics and statistics (qc, coverage)
  • Generating of final summary in Excel format containing relevant information obtained by the pipeline
  • Inicial preparation for GISAID submission
Assets 2
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