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martinghunt edited this page Jan 8, 2024 · 2 revisions

The first stage of Viridian is to map the reads to the reference genome and then choose the best matching primer scheme. It outputs a plot scheme_id.score_plot.pdf, from which the primer scheme scores are calculated. This is the plot for sequencing run ERR9362095:

ERR9362095 score_plot

For context, the scheme scores for this run are (for Viridian v1.1.0):

"scores": {
  "COVID-ARTIC-V3": 4518,
  "COVID-ARTIC-V4.1": 526,
  "COVID-ARTIC-V5.0-5.3.2_400": 280,
  "COVID-ARTIC-V5.0-5.2.0_1200": -56,
  "COVID-MIDNIGHT-1200": 358,
  "COVID-AMPLISEQ-V1": -248,
  "COVID-VARSKIP-V1a-2b": 250
}

It is clearly using amplicon scheme ARTIC version 3.

Next, it then makes the plot scheme_id.depth_across_genome.pdf, showing the read depth across the genome, with amplicons from the chosen scheme shown in alternating colours in the background.

This is the plot made from the same sequencing run ERR9362095:

ERR9362095 depth_across_genome

This is a very clean nanopore run, except for one missing amplicon around position 22.5kb. The dashed line marks the minimum depth required (default 20X), and the line plot is coloured red when it falls below the minimum depth.

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