Question

good scaffolder tool !

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8.3 years ago

midox ▴ 290

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

Assembly scaffold • 2.1k views

ADD COMMENT • link updated 8.3 years ago by dbrowne.up ▴ 80 • written 8.3 years ago by midox ▴ 290

Ram · Answer 1 · 2016-01-12

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8.3 years ago

dbrowne.up ▴ 80

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

ADD COMMENT • link 8.3 years ago by dbrowne.up ▴ 80

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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).

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 8.3 years ago by Chris Fields ★ 2.2k

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

ADD REPLY • link 8.3 years ago by midox ▴ 290

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'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).

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 8.3 years ago by Chris Fields ★ 2.2k

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

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 8.3 years ago by midox ▴ 290

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

ADD REPLY • link 8.2 years ago by Chris Fields ★ 2.2k