fastx_toolkit fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output Start of sequence (5' end) End of sequence (3' end)

**What it does** This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. -------- **Barcode file Format** Barcode files are simple text files. Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. Example:: #This line is a comment (starts with a 'number' sign) BC1 GATCT BC2 ATCGT BC3 GTGAT BC4 TGTCT For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). Sequences matching the barcode will be stored in the appropriate file. One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. The output of this tool is an HTML file, displaying the split counts and the file locations. **Output Example** .. image:: ./static/fastx_icons/barcode_splitter_output_example.png