Home

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 this review, a formal description of GenomeScope and smudgeplot is this publication.

Installation

For installation look at the README.

Documentation

The program has a single access point - the command smudgeplot:

usage: smudgeplot <task> [options]

These tasks allow you to extract k-mer pairs out of a k-mer database and generate smudgeplots.

We recommend mainly using the README file and smudgeplot's --help for details about all the tasks (smudgeplot --help to get all the tasks, and smudgeplot <task> --help for details about parameters).

Currently there are five tasks you can perform using smudgeplot:

smudgeplot cutoff            # Calculate meaningful values for lower kmer histogram cutoff.
smudgeplot hetmers           # Calculate unique kmer pairs from a FastK k-mer database.
smudgeplot peak_aggregation  # Aggregates smudges using local aggregation algorithm.
smudgeplot plot              # Generate 2d histogram; infer ploidy and plot a smudgeplot.
smudgeplot all               # Runs all the steps (with default options).

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.

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 one for another species; feel free to contribute or leave us a comment :-).

Version 0.5 Skylight:

• IN PROGRESS

Version 0.4 Arched:

• BGA24
• tutorial strawberry
• tutorial saccharomyces

Version 0.3 Oriel (ok for high coverage datasets):

• 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