finished the first draft
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@ -183,7 +183,9 @@ truth to evaluate other mappers (winno-cmp). Out of 1,378,092 reads with mapQ10
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alignments by Winnowmap2, minimap2 v2.22 could map all of them. 118 reads, less
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than 0.01\% of all reads, were mapped differently by v2.22. 51 of them have
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multiple identical best alignments. We believe these are more likely to be
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Winnowmap2 errors.
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Winnowmap2 errors. Most of the remaining 67 (=118-51) reads have multiple
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highly similar but not identical alignments. We are not sure what are real
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mapping errors.
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The two benchmarks above only evaluate read mappings without variations.
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To measure the mapping accuracy in the presence of SVs (sim-sv), we reproduced
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@ -207,10 +209,11 @@ better, too. However, we could not get lra to work well with dipcall, so did
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not report the numbers.
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Minimap2 spends most computing time on base alignment. As recent improvements
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in v2.22 do not change the base alignment algorithm, the new version has similar
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performance to older verions. Minimap2 is consistently faster than Winnowmap2
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by several times.
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in v2.22 incur little additional computing and do not change the base alignment
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algorithm, the new version has similar performance to older verions. It is
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consistently faster than Winnowmap2 by several times. Our simple heuristics can
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be as effective as more complex solutions on real data and may help the
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development of future sequence aligners.
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\section*{Acknowledgements}
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We thank Arang Rhie and Chirag Jain for providing motivating examples where
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@ -218,8 +221,6 @@ older minimap2 underperforms.
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\paragraph{Funding\textcolon} This work is funded by NHGRI grant R01HG010040.
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~\\*
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\bibliography{minimap2}
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\end{document}
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