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Old 02-09-2016, 12:40 AM   #1
Location: France

Join Date: Sep 2010
Posts: 27
Default Scaffolding tools for metagenomics ???

Im currently working on paired end data (2*150) to build a metagenomics assembly.

So far im using the combination of megahit to build contigs and soapdenovo for scaffolding. soapdenovo is not mainained anymore.

Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but its not opensource.

thanks for sharing your experience.


Last edited by danova; 02-09-2016 at 04:00 AM.
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Old 02-09-2016, 08:19 AM   #2
Location: Argentina

Join Date: Feb 2013
Posts: 19

We've been using Velvet-MetaVelvet for a same type of data set, and we are pretty happy with it.
Check steps at
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Old 03-21-2016, 03:45 AM   #3
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Location: Cambridge

Join Date: Sep 2010
Posts: 116
Lightbulb You can give Newbler a try, but proper matepair would be essential for good res...

Dear David,

Newbler assembler (v3 or v2.8) actually has quite good scaffolding module, provided you give it good and properly preprocessed (cleaned) data in the fastq format...

Also any tool is limited to the range of the input data (max. 1.2kb for illumina shotgun),
So a proper matepair (or 454 PE is a must, if yours repeats are longer than 900bp.

See bellow for more info:


Originally Posted by danova View Post
Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but its not opensource.

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Old 07-20-2016, 07:53 AM   #4
Location: Germany/Netherlands

Join Date: Feb 2014
Posts: 98

Opera also scaffolds.

It might be recommendable to first to binning on the contigs and afterwards the scaffolding, because it might lead to better results (due to less ambiguous mapping within the bins)
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metagenomics, scaffold, scaffolding

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