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Update README.md
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micahvista authored Sep 9, 2024
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Expand Up @@ -35,7 +35,7 @@ Usage
-mode H For aligning high error rate long read (Pacbio CLR, ONT).
-mode L For aligning low error rate long read (Pacbio HiFi).
-mode S Increase the sensitivity for small variants. (<100bp). (Pacbio CLR, ONT, HiFi).
-mode R Use a fixed value for the variation penalty that is more sensitive to translocation events, such as gene conversion. (Pacbio CLR, ONT, HiFi).
-mode R Use a fixed value for the variation penalty, more sensitive to translocation events, such as gene conversion. (Pacbio CLR, ONT, HiFi).
-k k-mer size (no larger than 28, deflaut: 15) # set -k 19 -w 10 for HiFi data
to reduce run time (2X faster) but there is very small decrease in accuracy.
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