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Old 07-18-2013, 04:36 AM   #1
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 )
2. Error correction (
3. Digital normalization ( -
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.wenger is offline   Reply With Quote

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