I am looking for any two strains of S. pneumoniae for which I can find their raw output sequencer data in FASTQ format and for which I can find their reference genomes (since I plan to align the raw data in the FASTQ format to the reference genomes using Bowtie 2). I know that I could make artificial FASTQ files using a generator but I need to work with data that came out of a real sequencer.

I tried looking in NCBI, Ensembl, and ArrayExpress and I did find reference genomes for some strains such as [R6][1] and [others][2]. However, finding the raw data straight out of a sequencer (FASTQ format) seems a hard task.

In summary, where can I find any two strains of S. pneumoniae for which can I find the aforementioned raw data (I assume that there must be popular strains for which this is more easily found than for others) along with their reference genomes?

 [1]: http://www.streppneumoniae.com/getntseq.asp
 [2]: http://strepneumo-sybil.igs.umaryland.edu/cgi-bin/current/shared/index.cgi?site=strepneumo
You can get FASTQ and FASTA [here][1].

Most strains will provide the raw data associated with the study. For example: http://www.ebi.ac.uk/ena/data/view/ERP000241

 [1]: http://www.ebi.ac.uk/ena/data/search?query=streptococcus%20pneumoniae