@@ -914,7 +914,64 @@ assemble all input data, at the expense of runtime.
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.. _corErrorRate:
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corErrorRate <integer=unset>
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Do not use overlaps with error rate higher than this (estimated error rate for `mhap` and `minimap` overlaps).
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Do not use overlaps with error rate higher than this when computing corrected reads.
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In Canu v2.2, this parameter was changed from 0.50 (for -nanopore) and 0.30
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(for -pacbio) to 0.30 and 0.25, respectively.
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The tables below show a significant speedup for Nanopore reads without much
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loss in output quantity. There is indication of a slight improvement in
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corrected read quality at lower corErrorRate, however, read quality was not
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directly evaluated.
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For PacBio reads, with a smaller change in corErrorRate, the speedup is
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about 10%.
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+-----------------+--------------------+------------------+-------------------+------------+
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| CHM13 Chromosome X, nanopore, 105x input coverage |
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+-----------------+--------------------+------------------+-------------------+------------+
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| | | | Corrected | | Trimmed | | Bogart | | CPU Time |
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| | corErrorRate | | Coverage | | Coverage | | Error Rate | | (hours) |
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+=================+====================+==================+===================+============+
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| 5 | 22.0x | 21.8x | 0.3958% | |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 10 | 35.7x | 35.2x | | |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 15 | 38.1x | 37.5x | | |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 20 | 38.6x | 38.0x | | 1160 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 25 | 38.7x | 38.1x | | 1290 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 30 | 38.8x | 38.1x | | 1449 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 40 | 38.8x | 38.1x | | 1625 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 50 | 38.8x | 38.2x | | 3683 |
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+-----------------+--------------------+------------------+-------------------+------------+
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+-----------------+--------------------+------------------+-------------------+------------+
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| HG002 Chromosome X, nanopore, 20x input coverage |
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+-----------------+--------------------+------------------+-------------------+------------+
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| | | | Corrected | | Trimmed | | Bogart | | CPU Time |
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| | corErrorRate | | Coverage | | Coverage | | Error Rate | | (hours) |
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+=================+====================+==================+===================+============+
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| 5 | --.-x | --.-x | -% | 31 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 10 | 3.9x | --.-x | -% | 66 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 15 | 9.6x | --.-x | -% | 105 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 20 | 11.4x | 11.2x | 1.71% | 134 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 25 | 11.9x | 11.6x | 1.79% | 154 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 30 | 12.0x | 11.8x | 1.83% | 169 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 40 | 12.2x | 12.0x | 1.94% | 221 |
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+-----------------+--------------------+------------------+-------------------+------------+
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| 50 | 12.6x | 12.3x | 2.29% | 709 |
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+-----------------+--------------------+------------------+-------------------+------------+
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corConsensus <string="falconpipe">
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Which algorithm to use for computing read consensus sequences. Only 'falcon' and 'falconpipe' are supported.
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