2.0.0

• [breaking change] This pipeline no longer does basecalling and barcoding inside the pipeline.
• Use Medaka by default instead of Nanopolish in artic
• Updated tools used by the pipeline
• Updated GISAID Excel template

1.6

Dependency updates

1.5

• Correctly handle variant when it has multiple words (e.g. "Probable Omicron").
• Moved pipeline own containers from DockerHub to GitHub Container Registry.

1.4

Dependencies updates mainly

1.3

• Software updates
• Dropped GISAID clade assignment, and added "Variant" as a column in output file
• Now collects software versions

1.2

Updated Nextclade and Pangolin

1.1

Simplified Guppy configuration

1.0

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