[BGI-SOAP:159] SOAPdenovo with heterogenous data

[Jared Price]

Hi all,
I am working on a project to do a full de novo assembly of a plant
genome. I was interested in SOAPdenovo because it is optimized for
short reads and for large genomes. However, not all of our sequencing
data is Illumina. We have a heterogenous data set that consists of 4
libraries. 1 library is Illumina WGS, 1 is 454 WGS, and then we have
2 paired-end libraries done on 454 (3kb and 20 kb respectively).
Would it be appropriate to try to assemble this data set using
SOAPdenovo?

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[Francesco Vezzi]

I Jerad
Do to the fact that most of your data is from 454 probably the best
thing you can do is to assemble the illumina lane with SOAPdenovo and
then assemble with newbler the 3 545 lanes and the resulting contig of
SOAP2. SOAP uses a de bruijn graph data structure that is well suited
for short illumina reads but it is not enough flexible in order to
handle 454 reads. Newbler, instead, is based on Overlap Layout Approach
that work well with long reads

Francesco