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Welcome to the smudgeplot wiki!

Documentation

The program has a single access point - a script called smudgeplot. Currently there are 4 different tasks you can call 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.
• map: Map kmers of individual smudges to a genome.

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.

Tutorials

We do have one a 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 :-).

• strawberry tutorial