Add BAM kinetics information

PacificBiosciences · Nov 17, 2020 · 3da9e7c · 3da9e7c
1 parent ac0f071
commit 3da9e7c
Showing 1 changed file with 30 additions and 22 deletions.
diff --git a/docs/faq/bam-output.md b/docs/faq/bam-output.md
@@ -6,20 +6,20 @@ title: BAM output
 
 ## What BAM tags are generated?
 
-|  Tag  | Type  | Description |
-| :---: | :---: | ----------- |
-| `ec`  | `f`   | [Effective coverage](/faq/accuracy-vs-passes#how-is-number-of-passes-computed)|
-| `fi`  | `B,C` | [Forward IPD (codec V1)](/faq/kinetics)|
-| `fn`  | `i`   | [Forward number of complete passes (zero or more)](/faq/kinetics)|
-| `fp`  | `B,C` | [Forward PulseWidth (codec V1)](/faq/kinetics)|
-| `np`  | `i`   | [Number of full-length subreads](/faq/accuracy-vs-passes#how-is-number-of-passes-computed)|
-| `ri`  | `B,C` | [Reverse IPD (codec V1)](/faq/kinetics)|
-| `rn`  | `i`   | [Reverse number of complete passes (zero or more)](/faq/kinetics)|
-| `rp`  | `B,C` | [Reverse PulseWidth (codec V1)](/faq/kinetics)|
-| `rq`  | `f`   | [Predicted average read accuracy](/how-does-ccs-work#9-qv-calculation)|
-| `sn`  | `B,f` | Signal-to-noise ratios for each nucleotide|
-| `zm`  | `i`   | ZMW hole number |
-| `RG`  | `z`   | Read group |
+| Tag  | Type  | Description                                                                                |
+|:----:|:-----:|--------------------------------------------------------------------------------------------|
+| `ec` |  `f`  | [Effective coverage](/faq/accuracy-vs-passes#how-is-number-of-passes-computed)             |
+| `fi` | `B,C` | [Forward IPD (codec V1)](/faq/kinetics)                                                    |
+| `fn` |  `i`  | [Forward number of complete passes (zero or more)](/faq/kinetics)                          |
+| `fp` | `B,C` | [Forward PulseWidth (codec V1)](/faq/kinetics)                                             |
+| `np` |  `i`  | [Number of full-length subreads](/faq/accuracy-vs-passes#how-is-number-of-passes-computed) |
+| `ri` | `B,C` | [Reverse IPD (codec V1)](/faq/kinetics)                                                    |
+| `rn` |  `i`  | [Reverse number of complete passes (zero or more)](/faq/kinetics)                          |
+| `rp` | `B,C` | [Reverse PulseWidth (codec V1)](/faq/kinetics)                                             |
+| `rq` |  `f`  | [Predicted average read accuracy](/how-does-ccs-work#9-qv-calculation)                     |
+| `sn` | `B,f` | Signal-to-noise ratios for each nucleotide                                                 |
+| `zm` |  `i`  | ZMW hole number                                                                            |
+| `RG` |  `z`  | Read group                                                                                 |
 
 
 ## How does the output BAM file size scale with yield?
@@ -45,11 +45,19 @@ 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:
 
-| BAM name             |        Options                             | Bytes/<br>Base | Bytes/<br>HiFiBase | Example<br>(GBytes) | Example<br>(GBytes) |
-| -------------------- | ------------------------------------------ | :------------: | :----------------: | :-----------------: | :-----------------: |
-| hifi.bam             |                                            | 0.7            | 0.7                | 100                 | 63                  |
-| hifi.hifikin.bam     | `--hifi-kinetics`                          | 3.7            | 3.7                | 528                 | 336                 |
-| reads.bam            | `--all`                                    | 0.55           | 1.1                | 157                 | 100                 |
-| reads.hifikin.bam    | `--all --hifi-kinetics`                    | 2.3            | 4.5                | 642                 | 409                 |
-| reads.allkin.bam     | `--all --all-kinetics`                     | 2.9            | 5.7                | 814                 | 518                 |
-| reads.allkin.sub.bam | `--all --all-kinetics --subread-fallback`  | 3.0            | 5.8                | 828                 | 527                 |
+| Read types                 | Kinetics                 | Options                                   | Bytes/<br>Base | Bytes/<br>HiFiBase | Example<br>(GBytes) | Example<br>(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`.