This gem is designed to demultiplex paired end reads produced by Illumina with Nugen barcodes. It is using FASTX Barcode Splitter from the FASTX-Toolkit for the barcode splitting.
nugen_barcode_splitter [options] -p project_dir -o out_dir -c sample_sheet_nugen
Example sample_sheet_nugen.csv :
FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
C0ED3ACXX,4,S1,hg19,ACCC,RNA Seq,N,,,33333
C0ED3ACXX,4,S2,hg19,GAGT,RNA Seq,N,,,44444
C0ED3ACXX,4,S3,hg19,CGTA,RNA Seq,N,,,33333
C0ED3ACXX,4,S4,hg19,TTAG,RNA Seq,N,,,44444
C0ED3ACXX,5,S5,hg19,AGGG,RNA Seq,N,,,33333
C0ED3ACXX,5,S6,hg19,GTCA,RNA Seq,N,,,44444
C0ED3ACXX,6,S7,hg19,CCAT,RNA Seq,N,,,33333
Note: The sample names must be alphanumerical!
-p, --project_dir Illumina project directory (../Unaligned/ProjectXXX/)
-o, --out_dir The desired output directory
-s, --sample_sheet Please provide your sample_sheet
-e, --end_of_line Limit the search for the barcode to the end of the line DEFAULT:false
-b, --begin_of_line Limit the search for the barcode to the start of the line DEFAULT:false
-k, --keep_barcode Do not trim of the barcode DEFAULT:false
-m, --mismatches NUM Number of mismatches (Default:1)
-n, --laneNumber NUM Specific lane number (Default:all lanes)
-x DIR,
--fastx_barcode_splitter.pl
-d, --debug Debug mode!
-h, --help Show this message
Since this gem is for pairend reads, the results of the FASTX Barcode splitter. The Nugen barcode can be found on the forward read at the beginning of each line (5' end).
This class makes sure the given file is in fastq format, when it is initialized. The method add enlarges the read by a given number of N's (base) and it also adds the lowest score of quality @ to the quality line accordingly.
This class delivers the templates for the different fastx_barcode_splitter.pl runs.
A class SampleSheet consists of sample_id's, barcodes and lanes. It also creates barcode.txt files for the fastq_multx part.
Statistics combines the log output into one statistic.