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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.
For installation look at README files.
The program has a single access point - a script called smudgeplot.py:
usage: smudgeplot.py <task> [options]
These tasks allow you to extract k-mer pairs out of a k-mer database and generate smudgeplot. We made quite a lot of changes recently and this wiki is not entirely up to data. Most of the ideas are the same between versions (e.g. FAQ still might be useful for you), but if you are interested in tutorials, make sure you find one that is for the version of smudgeplot you are running. We would recommend to look mainly at the README file and help of smudgeplot for details about all the tasks (smudgeplot.py --help to get all the tasks, and smudgeplot.py <task> --help for details about parameters).
If you discover any feature that would have missing, wrong, or even a strange description. open an issue or drop us an email.
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 0.4 Arched (currently recommended):
Version 0.3 Oriel (ok for high coverage datasets):
Version 0.2.5 Double hang with curtains (depreciated):
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