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What BAM tags are generated?

How does the output BAM file size scale with yield?

For each base, the output BAM file size scales as follows

  • 0.5 byte/base for the actual base (4-bit encoding)
  • 1 byte/base for the QV
  • 1 byte/base for the forward PW
  • 1 byte/base for the forward IPD
  • 1 byte/base for the reverse PW
  • 1 byte/base for the reverse IPD

For a normal ccs run without kinetics, the upper bound is 1.5 bytes/base. If ccs is run with kinetics, the upper bound is 5.5 bytes/base.

Per-read meta information add a fixed amount of 32 bytes per read:

  • ec,rq : float, each 4 bytes
  • sn: float array, 4x4 bytes
  • np, zm: int32_t, 4 byte
  • RG: string of length 8, 8x1 bytes

The actual output BAM that ccs generates is compressed. Compression is data-dependent and because of that, upper bounds can’t be provided. For a 19kb insert library and 30h movie time, the ccs BAM files scale on average with:

Read types Kinetics Options Bytes/
Base
Bytes/
HiFiBase
Example
(GBytes)
Example
(GBytes)
HiFi None   0.7 0.7 100 63
HiFi HiFi --hifi-kinetics 3.7 3.7 528 336
HiFi + LQ CCS + unpolished None --all 0.55 1.1 157 100
HiFi + LQ CCS + unpolished HiFi --all --hifi-kinetics 2.3 4.5 642 409
HiFi + LQ CCS + unpolished HiFi + LQ CCS --all --all-kinetics 2.9 5.7 814 518
HiFi + LQ CCS + fallback HiFi + LQ CCS + fallback --all --all-kinetics --subread-fallback 3.0 5.8 828 527

Legend:

  • HiFi - Polished CCS reads with predicted accuracy greater equals Q20, optionally with kinetics
  • LQ CCS - Polished CCS reads with predicted accuracy below Q20, optionally with kinetics
  • unpolished - Unpolished consensus sequence with two or fewer passes, no kinetics possible
  • fallback - One representative subread for ZMWs, instead of an unpolished consensus sequence, optionally with kinetics

The Sequel IIe system either runs with --all per default or optionally with --all --all-kinetics --subread-fallback.


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