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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,92 @@ | ||
| --- | ||
| layout: default | ||
| parent: FAQ | ||
| title: Mode --split-heteroduplex | ||
| --- | ||
|
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||
| # Attention: This is an early access feature! | ||
|
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| ## What is heteroduplex filtering? | ||
| Starting with _ccs_ v6.2.0, single-strand artifacts, such as insertions larger | ||
| than 20 bases, do not necessarily have to be filtered out. Using `--split-heteroduplexes`, | ||
| _ccs_ is able to split ZMW on-the-fly after detecting such heteroduplex and | ||
| process each strand separately. As a consequence, _ccs_ has to distinguish between | ||
| double-stranded (DS) and single-stranded (DS) ZMWs and their consensus reads. | ||
| Implications: | ||
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||
| * Single-strand reads are stored in an extra file | ||
| * Summary logs report double-strand and single-strand metrics | ||
| * `ccs_reports.txt` file contains two columns, double-strand and single-strand reads | ||
|
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| We are currently investigating how reliable we can detect indel and SNV | ||
| heteroduplexes and might add those to strand-aware splitting in future versions. | ||
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| ### Additional `*.stranded.bam` file | ||
| The file `outputPrefix.stranded.bam` contains all single-strand reads. Read names | ||
| follow the by-strand scheme with `/fwd` and `/rev` suffixes. There are up to two | ||
| reads per split ZMW. | ||
|
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||
| ### Summary logs | ||
| At the end of each execution, _ccs_ reports for `--log-level INFO` a summary. | ||
| This summary contains combined and individual metrics for DS and SS. | ||
|
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||
| ``` | ||
| ------------------------------------------------- | ||
| Summary stats abbreviations: | ||
| ZMW - A productive Zero-Mode Waveguide | ||
| DS - Double Strand | ||
| SS - Single Strand | ||
| DS-ZMW - All subreads were used from a single ZMW | ||
| SS-ZMW - ZMW is split into fwd and rev strands, | ||
| each strand is polished individually | ||
| DS-Read - CCS read of a DS-ZMW | ||
| SS-Read - CCS read of one strand of a SS-ZMW | ||
| HiFi - CCS reads with predicted accuracy >=Q20 | ||
| UMY - Unique Molecular Yield of all reads passing filters | ||
| HiFi Yield - UMY of >=Q20 DS- and SS-ZMWs, longest read per ZMW | ||
| ------------------------------------------------- | ||
| ZMWs Input : 53895 | ||
| ZMWs Written : 22684 | ||
| - DS / SS : 22644 / 40 | ||
| UMY : 413.2 MBases (6.8 GBases/hr) | ||
| - DS / SS : 412.4 MBases / 733.7 KBases | ||
| HiFi Yield : 413.5 MBases (6.8 GBases/hr) | ||
| - DS / SS : 412.4 MBases / 1.0 MBases | ||
| HiFi Reads : 22701 | ||
| - DS / SS : 22644 / 57 | ||
| HiFi Avg Size : 18.2 KBases | ||
| HiFi Avg QV : 30.2 | ||
| ``` | ||
|
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||
| ### Strand-aware `ccs_reports.txt` | ||
| Typical content of the strand-aware `ccs_reports.txt` file. Contrary to the | ||
| default output, this file does not report numbers in ZMWs, but actual DS and SS | ||
| reads. Accounting in SS ZMWs is not possible, as one strand might fail and the | ||
| other succeed. | ||
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||
| ``` | ||
| Double-Strand Reads Single-Strand Reads | ||
| Inputs : 53590 (99.43%) 609 (0.564%) | ||
| Passed : 22644 (42.25%) 57 (9.360%) | ||
| Failed : 30946 (57.75%) 552 (90.64%) | ||
| Tandem repeats : 461 (1.490%) 0 (0.000%) | ||
| Exclusive failed counts | ||
| Below SNR threshold : 870 (2.811%) 0 (0.000%) | ||
| Median length filter : 0 (0.000%) 0 (0.000%) | ||
| Shortcut filters : 0 (0.000%) 0 (0.000%) | ||
| Lacking full passes : 26226 (84.75%) 0 (0.000%) | ||
| Coverage drops : 30 (0.097%) 0 (0.000%) | ||
| Insufficient draft cov : 61 (0.197%) 310 (56.16%) | ||
| Draft too different : 0 (0.000%) 0 (0.000%) | ||
| Draft generation error : 173 (0.559%) 54 (9.783%) | ||
| Draft above --max-length : 0 (0.000%) 0 (0.000%) | ||
| Draft below --min-length : 0 (0.000%) 0 (0.000%) | ||
| Reads failed polishing : 0 (0.000%) 0 (0.000%) | ||
| Empty coverage windows : 3 (0.010%) 0 (0.000%) | ||
| CCS did not converge : 2 (0.006%) 0 (0.000%) | ||
| CCS below minimum RQ : 3581 (11.57%) 188 (34.06%) | ||
| Unknown error : 0 (0.000%) 0 (0.000%) | ||
| ``` |
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