How ReadTools handle barcode information

ReadTools handle automatically barcode information in the read name for FASTQ files with Illumina legacy and Casava formatting. For SAM/BAM/CRAM files, we assume that the sample barcode is encoded in the ‘BC’ tag as described in the SAM specifications. In case that these files were obtained from FASTQ files without ReadTools, it may be possible that the barcode is still attached to the read name. Please, use the option --barcodeInReadName for that input formats.

Barcode file format

The barcode file format of ReadTools follows the same format as the ExtractIlluminaBarcodes tool from Picard: tab-delimited table with named columns for including information. It could contain other columns, but the following are used for assigning Read Groups by barcode:

Required

  • barcode_sequence or barcode_sequence_1: sequence for the first barcode.
  • barcode_sequence_2: sequence for the second barcode in dual indexed libraries. Only required if more than one barcode is expected.
  • sample_name or barcode_name: name for the sample, which will appear in the SM Read Group field.

Optional

  • library_name: the name for the library, which will appear in the LB Read Group field.

Example file

sample_name	library_name	barcode_sequence	barcode_sequence_2
sample1 lib1	ATTACTCG	ATAGAGGC
sample2	lib2	TCCGGAGA	CCTATCCT
sample3	lib3	CGCTCATT	GGCTCTGA
sample4	lib4	GAGATTCC	AGGCGAAG
sample5	lib5	ATTCAGAA	TAATCTTA
sample6	lib1	GAATTCGT	CAGGACGT
sample7	lib2	CTGAAGCT	GTACTGAC
sample8	lib3	TAATGCGC	TATAGCCT
sample9	lib4	CGGCTATG	ATAGAGGC
sample1	lib5	TCCGCGAA	CCTATCCT