beta release

smudgeplots are right now

• production ready (fingers crossed)
• scaling for any genome size and read set (tested on a dataset of 1,000,000,000 kmers)
• fully automated (tested on set of 25 obscure genomes)
• equipped with rich set of warnings whenever the inference seems strange

pre-beta release

This is the first draft of automated smudgeplots - plots that reveal genome structure without any assumptions about assembly, mapping and base quality scores.

Right now we have:

• non-optimized python script to extract kmer pairs
• Rpackage and R scirpt to generate a smudgeplot out of the extracted kmers
• a small R smiplet to guess L/U thresholds for kmer filtering

Everything should be operational, but it was not extensively tested