smudgeplot

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sharing strange smudgeplot for imporve smudgeplot

1

hi, everyone i running smudgeplot for my data, get strange smudgeplot. look the below  i read the smudgeplot_warnings.txt, get information about provide the information for imporve the software. so...

ChenDepp

Bumps [numpy](https://github.com/numpy/numpy) from 1.16.2 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

long run time

5

Hi, my `smudgeplot.py hetkmers` job crashed multiple times because I ran out of memory. I manged to finally get it running by exclusively reserving an entire high memory node on...

beedatadriven

new smudgeplot mascot?

2


KamilSJaron

half genome length from tutorial-strawberry

4

This seems a silly question, but I really confused with why I get a half estimated compared to the tutorial with the same commands. So I have followed https://github.com/KamilSJaron/smudgeplot/wiki/tutorial-strawberry to...

fancyge

Repetitive mollusc genome interpretation

3

I have had some troubles understanding my smudgeplot of a highly repetitive genome that has undergone LTR expansion recently. I counted 21-mers from 10x linked reads with the barcode information...

mason-linscott

Previnting smudgeplot annotations with L / U too close to each other

1

Some people run into troubles (#55) for picking L and U too close to each other and then non-having any kmers with low minor allele coverage ratio. I don't necessarily...

KamilSJaron

make complete examples

8

We need some pilot examples that will go from raw reads to smudgeplot. We should do both those that are big and complicated as well as those that are small...

KamilSJaron

Generalized the middle_one_away function to make parallelization possible

3

As discussed in #65 I generalized the `middle_one_away` function to make parallelization possible. It is rebuilt as `get_pairs_at_pos` function and is now deterministic. Thus it contains a fix for #70...

RNieuwenhuis

explore other options how to identify heterozygous kmers

3

The smudgeplot is now limited for heterozygosity only to certain extend (we extract kemrs that are 1SNP from each other). If the divergence of haplotypes is too great, we are...

KamilSJaron