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Segmented Reads

A segmented read (S-read) is comprised of multiple fragments. The figure above shows an S-read with four fragments (Seq 1..4).

Segmented read names

For segmented reads, the base QNAME follows the CCS read conventions, while also appending the 0-based coordinate interval [qStart, qEnd) that represents its span within the HiFi read. If the HiFi read is split by strand the [qStart, qEnd) will follow the strand information.

  default:
  {movieName}/{holeNumber}/ccs/{qStart}_{qEnd}

  stranded:
  {movieName}/{holeNumber}/ccs/fwd/{qStart}_{qEnd}
  {movieName}/{holeNumber}/ccs/rev/{qStart}_{qEnd}

BAM tag	Type	Description	Example
di	i	Index of S-read	di:i:0
qs	i	qStart of segment in parent read	qs:i:16
qe	i	qEnd of segment in parent read	qe:i:450
dl	i	Leading adapter index	dl:i:0
dr	i	Trailing adapter index	dr:i:1
ds	b	binary json	ds:b:10,21,23

Notes:

• All tags of type i are 0-based
• qs and qe are left open, right closed
• dl and dr match the ordering of adapter sequences in the user input fasta
• ds contains a number of fields used for supporting skera undo, not intended for general use