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Old 02-08-2011, 12:08 AM   #1
tdoniger
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Location: Israel

Join Date: Nov 2010
Posts: 13
Default Vector Removal Software

I am trying to perform de novo assembly on 454 data using Newbler v2.5.

As a first stage, I need to remove the vector sequence. I have the vector sequence.

1. Using newbler, I have included the vector file both as a trimming database and as a screening database. Nonetheless, vector sequence is found in the assembly.

2. I have tried using Lucy. It does remove some of the vector sequences, but then using BLAST I still find quite a bit that was not removed.

2. I tried using SeqClean -which actually manages to remove all the vector but does not provide a quality file. I could write some program that would produce a modified .qual file, but I was wondering if such a tool already exists.

What are others experience in vector removal?

Much Thanks,
Tirza Doniger
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Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
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