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Old 07-18-2013, 04:36 AM   #1
yvan.wenger
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Location: Switzerland

Join Date: Aug 2009
Posts: 30
Default Illumina reads pretreatmentS before de-novo transcriptome assembly

Hello everybody,

Lately with datasets of >1bio 100 bp SE reads, I have been using these steps to do de-novo assembly of a complex eukaryotic genome (without a good quality genome, diploid with a high degree of single nucleotide polymorphism, which further complicate the assembly):

1. Adapter removal (I usually use adaperRemoval http://www.ncbi.nlm.nih.gov/pubmed/22748135 )
2. Error correction (http://sb.cs.cmu.edu/seecer/)
3. Digital normalization (http://arxiv.org/abs/1203.4802) -
I then usually assemble using velvet/oases

Individually I made some test and found all of these steps efficients and useful, but I guess I am not involved enough in the details of algorithms used to come up with a optimal order in which to use them.

In your opinion, is the order I*propose a good one to produce a decent transcriptome ?

In advance, many thanks for your insights !

Yvan
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