How to trim 454 low quality sequences

biohumin · 07-11-2010, 08:21 PM

Hi everybody:
I have got a run of 454 Titanium sequences, however i found there has a few bases whose quality is below 20. Is there has any software to trim the bad bases or sequences? Thank you.

Jose Blanca · 07-12-2010, 11:04 PM

Hi, our ngs_backbone software does that.

maubp · 07-13-2010, 04:43 AM

Why do you want to do the trimming? Isn't the Roche pipeline already trimming off the poor quality bits of the reads?

Where do you want to do the trimming? What I mean is, do you want to work with the SFF file, FASTA+QUAL, or maybe FASTQ files? Would you be interested help to write a python script doing this using Biopython?

Jose Blanca · 07-13-2010, 05:32 AM

@maubp

Well, the quality of the sequences released by some 454 services is quite questionable and it is worth to take a look and to trim some more.
If you want to take a look at how ngs_backbone does it you can do it, it's python code and it's based on biopython and on lucy.

maubp · 07-13-2010, 09:14 AM

@Jose - Understood. I was really wondering if the OP was looking at the untrimmed output from the SFF file (with all the poor quality regions included) rather than the trimmed output (where Roche will have removed most of the rubbish).

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07-11-2010, 08:21 PM	#1
biohumin Junior Member Location: china Join Date: Jul 2008 Posts: 4	How to trim 454 low quality sequences Hi everybody: I have got a run of 454 Titanium sequences, however i found there has a few bases whose quality is below 20. Is there has any software to trim the bad bases or sequences? Thank you.

07-12-2010, 11:04 PM	#2
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	Hi, our ngs_backbone software does that.

07-13-2010, 04:43 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Why do you want to do the trimming? Isn't the Roche pipeline already trimming off the poor quality bits of the reads? Where do you want to do the trimming? What I mean is, do you want to work with the SFF file, FASTA+QUAL, or maybe FASTQ files? Would you be interested help to write a python script doing this using Biopython?

07-13-2010, 05:32 AM	#4
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	@maubp Well, the quality of the sequences released by some 454 services is quite questionable and it is worth to take a look and to trim some more. If you want to take a look at how ngs_backbone does it you can do it, it's python code and it's based on biopython and on lucy.

07-13-2010, 09:14 AM	#5
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	@Jose - Understood. I was really wondering if the OP was looking at the untrimmed output from the SFF file (with all the poor quality regions included) rather than the trimmed output (where Roche will have removed most of the rubbish).