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Update README.md
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cjain7 authored Apr 29, 2020
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Expand Up @@ -45,7 +45,7 @@ For either mapping long reads or computing whole-genome alignments, Winnowmap re

winnowmap -W bad_k19_mers.txt -cx asm5 asm1.fa asm2.fa > output.paf
```
In this case, it may be useful to visualize the genome-to-genome dot plot. This [perl script](https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot) can be used to generate a dot plot from paf-formatted output.
In this case, it may be useful to visualize the genome-to-genome dot plot. This [perl script](https://github.com/marbl/MashMap/blob/master/scripts) can be used to generate a dot plot from paf-formatted output.

In all the three use-cases, the k-mer counting step using meryl is kept consistent with the mapping step. For example, ONT reads are mapped with k-mer length 15, where as PacBio reads are mapped with homopolymer-compressed k-mers of length 19. This is consistent with `map-ont` and `map-pb` presets of minimap2. In all use-cases, pre-computing repetitive k-mers using [meryl](https://github.com/marbl/meryl) is quite fast, it typically takes 2-3 minutes for the human genome reference.

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