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

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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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Old 02-08-2011, 01:51 AM   #2
ulz_peter
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In case you've got a fasta and a qual file you could merge them to a fastq file and then clip the vector sequences with the FastX package using FastX clipper:

http://hannonlab.cshl.edu/fastx_toolkit/

That worked quite well for me for removing Tranposon DNA elements from Library prep.
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Old 02-08-2011, 08:07 AM   #3
kmcarr
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Quote:
Originally Posted by tdoniger View Post
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.
Much Thanks,
Tirza Doniger
Tirza,

SeqClean includes a utility to create a new qual file which corresponds to your cleaned reads. The program is called 'cln2qual' and it is in the main seqclean directory. It takes as input the cleaning report generated by SeqClean (the .cln file) and your original .qual file. It outputs a new .qual file with appropriately trimmed (or excluded) qual scores.

Last edited by kmcarr; 02-08-2011 at 08:13 AM. Reason: Removed comments about read ordering in new qual file; mistaken about this.
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Old 02-08-2011, 11:29 PM   #4
tdoniger
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Wow! Thank you! Just what I was looking for! The 'cln2qual' tool works great. I didn't notice it in the SeqClean directory. Newbler accepts the input without any problems.

Thanks again,
Tirza
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