How do sequencing errors affect de Bruijn graphs?

[samanta]

This is another introductory article that some of you may find useful. You may wonder about what determines the RAM size required by de Bruijn assembly programs. In the following article, I showed that when reads have no error (imaginary world), size of de Bruijn depends on the genome, not the depth of sequencing.

http://www.homolog.us/blogs/?p=171

In this follow up post, I show how read errors affect sizes of de Bruijn graphs -

http://www.homolog.us/blogs/?p=190

Hopefully the above comments will help you find new ways to optimize available RAM, because not everyone can afford 512GB machines.

[pmiguel]

Seems like one way would be to use quality values of the sequence data. Trivially this could be used to hard mask the bases that are scored below a certain threshold.

--
Phillip

[rskr]

What assemblies from heterozygous individuals?