BWA or Bowtie2 are the most commonly used. You might also give a look to this web site: http://seqanswers.com/

Thanks a lot Fabio Marroni,

I am not able to get the meaning of your answer. What I mean to say is, I have a raw read dataset and I want to filter out the reads with low quality score and also adapter and primer contaminated reads. So is there any softwares or tools available for these job?

Thanks in advance........

Sorry! I misunderstood the question! Well, I usually use ERNE filter to remove contaminants and cutadapt to remove adapters. Hope this helps!

You can also try the Galaxy server. That is a cloud based "suite" of programs. Most of the freely available aligners are available on Galaxy. Similarly quality assurance and filtering programs are also available. Moreover, they have good set of tutorials, so you should be able to start off nicely.

Seqanswers (as has been mentioned earlier by Fabio) is a good resource. Similarly you want to check out http://www.biostars.org/, that is also a question answer forum and probably much active than here.

Good luck.

You could also consider using QIIME for this.

http://qiime.org/index.html

It's a package developed for bacterial 16S rRNA reads, but it has a functionality to do quality filtering of Illumina reads.

http://qiime.org/tutorials/processing_illumina_data.html#illumina-quality-filtering

Good luck!

Take a look to picard: http://picard.sourceforge.net/

Good Luck!