Quarto template an app. note

[MatthewRalston]

Using a PLOS template from quarto-journals to write up a preprint about kmerdb and the project. Early commits to version control may not be representative of the work.

What are the key aims of the preprint?

• 1. Submit to the reader rationale for working on kmers in Python in a clean(er) and more reproducible manner the analysis of k-mer profiles, indices, and their aggregates in grouping and quantifying similarity between species, tissues, or treatment conditions.
• 2. Suggest to the reader key statistics and advantages to precalculating them with kmerdb, then running interactive scripts with khmer, kPAL, or Jellyfish, all of which require counts be calculated at runtime, although indexes and data structures may be processed a priori.
• 3. Demonstrate uses of the correlation coefficient, matrix dimensionality reduction features, and clustering features to effect a metagenomic or ecologically inspired example.