Kamil S. Jaron

new smudgeplot mascot?

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

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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...

make complete examples

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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...

explore other options how to identify heterozygous kmers

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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...

Paralelization of the kmer search

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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...

Bad examples of smudgeplot

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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...

Update wiki

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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...

set up travis testing

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Set up a travis for integration testing

Check and fail if input reference is gzip compressed

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Hello, Thanks for making Manta! I just run `manta` in a cluster environment and after quite a lot of computation (2.5h using 32 cores), it started to complain that it...

thank you

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I don't have an issue, I am just really grateful you wrote this! I was so frustrated trying to generate a gap file and it was so much easier to...