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Old 01-03-2011, 12:09 PM   #1
Location: Davis, CA

Join Date: Mar 2009
Posts: 82
Default Quality trimming fastq 454 data?

Hi everyone,

Does anyone have suggestions for methods and parameters for effective quality trimming / filtering of 454 data? I have .fastq format data (no sff files )and would like to end trim and remove homopolymers. I don't need a complicated pipeline for other steps, as I've already barcode sorted and trimmed out adapter sequence.

I have tried using FASTX toolkit's fastq_quality_filter which doesn't seem to be working properly, since it fails to remove some parts of the sequence below my set threshold. Has anyone else had this problem? Should I only be using this tool on my Illumina data?

Thanks in advance!
ewilbanks is offline   Reply With Quote
Old 04-13-2011, 07:36 AM   #2
Location: Hong Kong

Join Date: Oct 2010
Posts: 74

Hi ,I studied the same data as you.You can use Galaxy's Build base quality distribution whcih can draw base quality distribution.and then you can saw your data's quality.Generally, That beginning of 5'&3' sequence usually are bad quality.

I want to ask you how to trim adapter? I saw FASTX-TOOLKIT can handle it,but the default dummy adapter. Does it apply to 454's data?
louis7781x is offline   Reply With Quote
Old 04-14-2011, 10:45 PM   #3
Location: Bad Nauheim, Germany

Join Date: Feb 2011
Posts: 31

I tried prinseq-lite ( for quality filtering. It is also able to trim x bases from the end or beginning, perhaps suitable for you!
Jenzo is offline   Reply With Quote

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