Documentation for kmer-ord
Documentation is still under development, bare with us
This documentation describes the kmer-ord toolkit for computing, normalising, and ordinating k-mer count data for exploratory analysis of long-read sequencing datasets or assembled contigs.
The workflow consists of:
- Generating k-mer count matrices
- Preprocessing the count matrix with appropriate normalisation for compositional data
- Performing dimensionality reduction
- Inspecting embeddings structure and binning
Documentation structure
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Getting started
Install dependencies and set up environment
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Reference
Complete command-line and parameter documentation for each script
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Tutorials
Practical guides for common workflows and analyses Workflows
Detailed examples Tutorials
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Concepts
Background material explaining why certain steps are required and how to interpret results.