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wtsi-hpag / Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
MIT License
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Recommended -blocks setting #7

Open cabbagesofdoom opened 5 years ago

cabbagesofdoom commented 5 years ago

Hi,

In the docs, you say:

The block value is very important. The default value of 2500 is very conservative and you may increase this value to say 5000 or 10000 to improve the length of scaffolds;

In your example command, you set: -block 50000 - bigger still.

Please, could you point me to a description of what this setting actually does, given that it is very important, and explain why the example is so much bigger than the recommendations?

Thanks!

Rich

foala commented 5 years ago

Hello, I have the same question The doc says the default is 2500, but the parameters say it is 50000. Could you please explain.