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Welcome to the smudgeplot wiki! The basic idea is to visualize kmer pairs that are similar, most likely homologous, to understand the genome structure. The tool intended for genome profiling (assembly-less understanding of genomes from sequencing reads) in combo with Genomescope. A good introduction to the whole idea of genome profiling is the manuscript introducing the two tools.

Installation

Check installation wiki page.

Documentation

The program has a single access point - a script called smudgeplot.py:

usage: smudgeplot.py <task> [options]

Currently there are three different tasks you can perform using the program:

• cutoff: Calculate meaningful values for lower/upper kmer histogram cutoff.
• hetkmers: Calculate unique kmer pairs from a Jellyfish or KMC dump file.
• plot: Generate 2d histogram; infere ploidy and plot a smudgeplot.

For specific questions you can check FAQ. If you discover any feature that would have missing, wrong, or even a strange description. open an issue or drop us an email.

Running smudgeplot

Check everything about input data for smudgeplot. Or follow the one nice tutorial guiding the analysis all the way from raw reads to the final smudgeplot. If you feel like making a new one, or if you wish us to try make another species; feel free to contribute or leave us a comment :-).

Version 0.2.5 Double hang with curtains:

• tutorial strawberry
• tutorial saccharomyces

Version 0.2.99 Pre-release of Oriel:

• BGA23

Citation

Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun 11, 1432 (2020). https://doi.org/10.1038/s41467-020-14998-3