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Old 03-01-2011, 06:44 AM   #1
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Location: Boston

Join Date: Mar 2011
Posts: 2
Default Assembling De Novo 454 Transcriptome Contigs and Singletons with Illumina Short Reads

Background: I have assembled 4 million None Normalized 454 Titanium de novo transcriptome Reads using Newbler 2.5, and have gotten amazing results, 88000 contigs with N50 of 951 bp, 35000 isotigs with N50 1500 longest being 7900, and 276564 singletons. Now I am about to sequence the same transcriptome using Illumina 75+ bp platfrom.
Problem: I am contemplating the assembly software that I should be using.
I really like newber's isoform prediction, and am not sure if it possible to merge both sets of raws reads together in an good assembly.
I haven't seen any software out that are able to utilize a transcriptome reference for assembling new reads
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