GBS barcode splitter Files

Usage: 
GBS_barcode.pl yourBarCodeFile yourEnzymeFile

You will need to create two text files first, a barcode file and an enzyme file.
Barcode File Example:
SampleName	code	paired	file
s1	CTCC	s	s_3_qseq.txt
s2	TGCA	s	s_3_qseq.txt
s3	ACTA	s	s_3_qseq.txt
s4	GTCT	s	s_3_qseq.txt
s5	GAAT	s	s_3_qseq.txt
s6	GCGT	s	s_3_qseq.txt
s7	TGGC	s	s_3_qseq.txt
s8	CGAT	s	s_3_qseq.txt
s9	CTTGA	s	s_3_qseq.txt
s10	TCACC	s	s_3_qseq.txt
s11	CTAGC	s	s_3_qseq.txt
s12	ACAAA	s	s_3_qseq.txt
s13	TTCTC	s	s_3_qseq.txt
s14	AGCCC	s	s_3_qseq.txt


Enzyme File Example (ApeKI):

Enzyme: C[AT]GC
FinalSize: 64
Ends: GCTGGATC,GCAGGATC,GCTGAGAT,GCAGAGAT,GCAGC,GCTGC
EnzymeEndSize: 4


Note:
1. If you works in Linux or Mac environment, you can use gzip compressed Illumina files directly, as long as the file names end with .gz.
2. In barcode file, "s" refere to single end Illumina data, "p" refer to paired end Illumina data. For paired end data files, you only need to provide the first file (with _1 in file name). The second file should have "_2" in file name, and will automatically be recognized.
3. In the enzyme file, you are required to provide final size. If reads are shorter than the final size after trimming of the barcode and 3' adapter, the read will be padded with "N" at 3' end. 
4. Some sample enzyme files are provided here.