fastqc with 454?

[newbie25]

Hi, I'm new to bioinformatics and have just received my first 454 data set (YAY!) I have been told that fastqc is a great program for visualizing the quality of your data and getting a good summary but it seems to be only for illumina reads? Can I use it for 454 reads if I convert them to fastq?
Thanks in advance!

[raonyguimaraes]

Yes you can! Here is an example of a report:

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/454_SRR073599_fastqc/fastqc_report.html

I'm trying to find a real good example, like this one for Illumina, anyone ?

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/good_sequence_short_fastqc/fastqc_report.html

[simonandrews]

If someone has a good 454 dataset they'd be prepared to share (or even point to in SRA) then I'm happy to expand the list of example reports on the FastQC homepage. I'm actually working on a more systematic analysis of public data with the tool but I'm happy to put up more examples in the short term if people would find that useful.

[raonyguimaraes]

Hi Simon, thanks for you reply.

I got a similar report of my reads from 454 with the example you are providing on your website.

I would like to know what are the recommended tools to trim my reads based on the quality of my initial report. Them I could make the before/after report and test if this is really helping to improve my assembly and annotation in someway.

I know I can do this with some scripts in python or perl but I would like something more ready2go.

Found this tool that looks promising: http://bioinf.comav.upv.es/ngs_backbone/cleaning.html

What are your suggestions for this trimming before the assembly?