Haplotagging

Unlike the other listed chemistries, haplotagging is a non-commercial (DIY) linked-read chemistry. Haplotagging barcodes are combinatorial and are made up of four 6bp segments. Two of these segments ("A" and "C") are the first 12bp of the I1 read and the other two ("B" and "D") are the first 12bp of the I2 read, both of which are provided by Illumina for standard sequencing runs. Because of this segment design, there are 96^4 (~84 million) possible barcode combinations (~900,000 per sample). The barcodes are stored in the sequence header under the BX:Z SAM tag, recoded in their "ACBD" format.

Specification

• 4 barcode segments
  • A segment is the first 6bp of the I1 read
  • C segment is the next 6bp of the I1 read (7-12)
  • B segment is the first 6bp of the I2 read
  • D segment is the next 6bp of the I2 read (7-12)
• barcode stored as BX:Z tag in the read header in ACBD format
  • e.g. @A003432423434:1:324 BX:Z:A45C01B84D21
• invalid barcode segment encoded with 00 (e.g., C00)