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Old 08-18-2016, 07:35 PM   #1
ronaldrcutler
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Location: Virginia

Join Date: May 2016
Posts: 80
Default De novo Assembly k-mer question

Hello all, I have a general discussion question:

If small kmers are used in an assembly that utilizes a de bruijn graph, we can expect to get many more contigs than we would if we used larger kmers. However, with smaller kmers, the contig quality is usually higher, sorting out repetitie elements, etc.

In the assembly pipeline, when scaffolding, we are using the paired-end reads to essentially put together fragments that may not have had enough coverage or overlap to join in the assembly. My question is: if we use small kmers in the initial assembly and then scaffold, will this result in the same amount of scaffolds if we were to use larger kmers in the initial assembly and then scaffold? What is the effect on the contig quality - if any?

Cheers
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