[Bio-Linux] FastQC tool for checking high throughput sequence data

[Tim Booth]

Hi All,

Today we've been playing with the FastQC tool from the Babraham
institute.  It takes the .fastq file you get from an Illumina run and
makes some nice reports and graphs to let you visualise various metrics
for your sequences and assess the quality.

Downloading and running the tool is fairly easy but I've made a
Bio-Linux package that comes with the added convenience of an icon
appearing in the Bioinformatics menu, so you may want to use that
instead:

apt-get install bio-linux-fastqc

We had some 454 data to analyse and it was saved as separate .fasta
and .qual files which needed to be converted to a single .fastq file for
FastQC.  If you need to do the same, there are some handy conversion
scripts now on the website:

http://nebc.nerc.ac.uk/tools/code-corner/scripts/sequence-formatting-and-other-text-manipulation

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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