Nonpareil

Nonpareil uses the redundancy of the reads in a metagenomic dataset to estimate the average coverage and predict the amount of sequences that will be required to achieve “nearly complete coverage”, defined as ≥95% or ≥99% average coverage.

Since Nonpareil main output has no model information, it is necessary extract the curves object as a JSON file. From version v3.5.5 this can be done with an auxiliary R script, briefly:

NonpareilCurves.R --json out.json model.npo

Module config options

The module plots a line graph for each sample, with a tab panel to switch between only observed data, only models, or both combined (model with a dashed line). It will use the colors specified in the JSON file by nonpareil and, if some is missing use one from a MultiQC colour scheme (default: Paired) that can be defined with:

nonpareil:
  plot_colours: Paired

File search patterns

nonpareil:
  - contents: LRstar
    fn: "*.json"
    max_filesize: 1048576
    num_lines: 50