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good scaffolder tool !

hello,
Can you suggest me a good scaffolder please?
thankyou

assembly scaffold
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updated by dbrowne.up • dbrowne.up • written by midox midox

1 answer

BESST, SSPACE, SOPRA, and OPERA are some commonly used scaffolding tools. See this paper for a more detailed analysis of scaffolding tools: http://www.genomebiology.com/2014/15/3/R42

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written by dbrowne.up • dbrowne.up

I should add, the scaffolder you choose also depends on the type of data you are using for scaffolding. Long reads can be used for scaffolding using SSPACE-LongRead and PBJelly2 (which also will gap fill).

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updated by Ram Ram • written by Chris Fields Chris Fields

you mean I need SPACE-Long Read and PBJelly together or just SPACE-LongRead OR PBJelly2 ??
thanks

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written by midox midox

'Or'. PBJelly2 does have additional gap-filling functionality as well and is what I generally use (though I understand this is to be added to SSPACE-LongRead).

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updated by Ram Ram • written by Chris Fields Chris Fields

okey, So I use SPACE-Long Read + PBJelly?

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updated by Ram Ram • written by midox midox

I tend to use multiple tools to find what works best, followed by QC (generally Reapr) to ensure the joins are fine.

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written by Chris Fields Chris Fields

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