For fastq QC and trimming...have a look at the FASTQC tools they are excellent. If you want to play around with it you can use the fastqc but also the fastX toolkit as well as bowtie/tophat on the public usegalaxy.org server.

Usually bowtie and other mappers/assemblers use the quality scores per base. FASTA doesn't have it *unless you have an accompanying .qual file (i.e. from 454). At usegalaxy you can interconvert sff, fasta+qual with fastq and such as well.

PS: Why did you trash the quality scores on the first place? Your title says fastq -> FASTA...why?

PPS: I do not work at usegalaxy and do not get paid to promote it :-)! But I like the reproducible framework and locally it improved our tool sharing.