smudgeplot

smudgeplot copied to clipboard

Non deterministic behaviour of middle_one_away function

8

**What did you do** I ran `smudgeplot.py hetkmers -o Test_middle --middle K_mer_kmc_db_k_21_L15_U220.dump` 4 times in a row on [this](https://filesender.surf.nl/?s=download&token=ca313237-d837-4725-9a5f-9897ac5df43b) 2.5gb dump file. ` wc -l Test_middle_?_coverages.tsv` gives ``` 659425 Test_middle_1_coverages.tsv...

RNieuwenhuis

add `--extreme_ploidies` flag

1

This pull request adds a flag to increase the ymax threshold of `10*draft_n` in case of extremely high ploidies. I am not sure if it's worth adding, but here is...

cmdoret

Using smudgeplot with very high ploidy levels

4

Hi Kamil, Thanks for the clear documentation and awesome tool. I have troubles understanding my smudgeplot. I have used follwing command to generate it ``` smudgeplot.py plot kmcdb_L135_U1000_coverages.tsv -k 21...

cmdoret

Paralelization of the kmer search

6

Hi @KamilSJaron , I was wondering how the parallelization you tried was implemented. Because I also saw in a different thread that you tried to create smudgeplots based on heterozygosity...

KamilSJaron

Bad examples of smudgeplot

3

A collection of smudgeplots that went wrong... (a material for a wiki page showing potential pitfalls) Types of problems: - a problem of input data - a problem of input...

KamilSJaron

Update wiki

2

for notes about what to update in the wiki Explain why to look at the both plots at the same time might be the only way how to make meaningful...

KamilSJaron

set up travis testing

1

Set up a travis for integration testing

KamilSJaron

Could I use to these AAB kmer to make evaluation the assembled phased genome?

2

I have troubles understanding my smudgeplot. it look like this:  How to classified the kmer pairs into AA and AB from the results ? Could I use to theses...

liufuyan2016

Interpretation of smudgy smudgeplot for diatom genome

1

My group is working on sequencing the genome of a freshwater diatom, one member of a large class of unicellular algae. We have no previous knowledge or indication of its...

sarahfrail

solve speckiness problem of smudgeplot

1

KamilSJaron