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Welcome to the smudgeplot wiki! The basic idea is to visualize kmer pairs that are really similar, most likely homologous, to understand genome structure.
Check installation wiki page.
The program has a single access point - a script called smudgeplot:
usage: smudgeplot <task> [options]
Currently there are four 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.
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 :-).