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Old 06-18-2010, 02:46 AM   #53
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 870
Default FastQC v0.4 released

I've just put FastQC v0.4 up on our website.

FastQC v0.4 introduces a new analysis module, an easier way to launch the program from the command line and a new output file, as well as fixing a few minor bugs.

The new analysis module is the sequence duplication level module. This is a complement to the existing overrepresented sequences module in that it looks at sequences which occur more than once in your data. The new module takes a more global view and says what proportion of all of your sequences occur once, twice, three times etc. In a diverse library most sequences should occur only once. A highly enriched library may have some duplication, but higher levels of duplication may indicate a problem, such as a PCR overamplification.

In response to several requests we've also now introduced a new output file into the report. This is a text based, tab delimited file which includes all of the data show in the graphs in the graphical report. This would allow people
running pipelines to store the data generated by fastQC and analyse it systematically rather than just taking the pass/fail/warn summary, or reviewing the reports manually.

Finally, if you're running fastqc from the command line we've now included a 'fastqc' wrapper script which you can launch directly rather than having to construct a java launch command. You can still pass -Dxxx options through to the program, but for simple analyses you can now simply run:

fastqc [some files]

..once you have included the FastQC install directory into your path. More details are in the install document.

You can get the new version from:

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

[If you don't see the new version of any page hit control+refresh to force our cache to update]
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