I have thousands sequencing files, in those files, there are 4 different files: three different barcodes and one background, I try to split them by "barcode spliter" application, but it's not work because the barcodes randomly exist in the sequence text, I think perhaps I need a alignment application to recognize my barcode in the text files, can any suggestion given to solve this problem?
True, the barcode splitting will not work for your use case. Instead, try the tool NGS: Mothur > Trim.seqs.
There is a link near the bottom of the tool form to the Mothur wiki that can help with usage. And a Galaxy tutorial using the tool suite as an example is here: http://galaxyproject.github.io/training-material/topics/metagenomics/
Hope this helps! Jen, Galaxy team