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Trimmomatic offers similar options to Flexbar with the potential benefit that many illumina adaptor sequences are already "built-in". It is available here.
More Example Data
See if you can figure out what's wrong with these data sets (copy them to your $SCRATCH directory before analyzing them) and then process them to get rid of the problem(s):
Example #1: Single-end data
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$BI/gva_course/read_processing_example/JJM104_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz |