sequence filtering

[scalabrin]

you can also see rNA, it is mainly an aligner but does also a good job on sequence filtering (you need to construct a database of sequences to be filtered) and quality trimming

http://iga-rna.sourceforge.net/

As the manual is not that good you can ask help to the developer, delfabbroATappliedgenomics.org

Vezzi F., Del Fabbro C., Tomescu A.I., and Policriti A. rNA: a Fast and Accurate Short Reads Numerical Aligner. Bioinformatics, Vol.28, Issue 1, January 2012

or

http://bioinformatics.oxfordjournals.org/content/early/2011/11/13/bioinformatics.btr617

I personally used to filter out a set of bacterial sequences and it worked pretty well

[mattanswers]

You can see if DeconSeq will help:

http://deconseq.sourceforge.net/

[yaximik]

Hi

This may be a silly question, but I am wondering if there are some tools available to do broad category filtering? I am dealing with ancient DNA that comes from excavated samples and thus is heavily contaminated with all kind of bacteria. With all precautions against contamination the majority of reads are still of the bacterial origin from all kind of bacteria imaginable, which makes futile attempts to set up narrow filters. Is there a better way to filter at least most of bacterial sequences?