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
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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