Hello, so I have a simple question, what programs can you use to open and read FASTQ files?
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Fastq files are text. So in principal you can use a text editor to open the file (or use cat/more utilities to look at the contents).
In general you will want to do QC/Trimming/Pre-processing/Alignments using the fastq files to do secondary data analysis.
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There are links for each of the programs in my post above. If you do not see them then temporarily disable "no script" or any other similar plugin that you may be using to see the links.
QC: http://www.bioinformatics.babraham.a...ojects/fastqc/
Trimming: http://www.usadellab.org/cms/?page=trimmomatic
Pre-processing: http://en.wikibooks.org/wiki/Next_Ge...Pre-processing
General Analysis: http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29
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