Please see the tools under "NGS: QC and manipulation". You will need the dataset assigned to a .fastqsanger "datatype" before using it with most tools (scale the quality scores to Sanger Phred+33).
- Combine FASTA and QUAL - merge
- Fastq Groomer - scale quality scores, assign datatype
This tool section has been reorganized. Any tools that were in this location previously, but that are no longer supported on the public Main Galaxy instance (http://usegalaxy.org), can be found in the Tool Shed (http://usegalaxy.org/toolshed) for use in a local or cloud Galaxy (http://wiki.galaxyproject.org/BigPicture/Choices).
Thanks! Jen, Galaxy team