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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 CCS read. If the CCS read is split by strand

  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 read segment 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

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