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finished the first draft

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Heng Li 2021-08-07 00:33:31 -04:00
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@ -183,7 +183,9 @@ truth to evaluate other mappers (winno-cmp). Out of 1,378,092 reads with mapQ10
alignments by Winnowmap2, minimap2 v2.22 could map all of them. 118 reads, less alignments by Winnowmap2, minimap2 v2.22 could map all of them. 118 reads, less
than 0.01\% of all reads, were mapped differently by v2.22. 51 of them have than 0.01\% of all reads, were mapped differently by v2.22. 51 of them have
multiple identical best alignments. We believe these are more likely to be multiple identical best alignments. We believe these are more likely to be
Winnowmap2 errors. Winnowmap2 errors. Most of the remaining 67 (=118-51) reads have multiple
highly similar but not identical alignments. We are not sure what are real
mapping errors.
The two benchmarks above only evaluate read mappings without variations. The two benchmarks above only evaluate read mappings without variations.
To measure the mapping accuracy in the presence of SVs (sim-sv), we reproduced To measure the mapping accuracy in the presence of SVs (sim-sv), we reproduced
@ -207,10 +209,11 @@ better, too. However, we could not get lra to work well with dipcall, so did
not report the numbers. not report the numbers.
Minimap2 spends most computing time on base alignment. As recent improvements Minimap2 spends most computing time on base alignment. As recent improvements
in v2.22 do not change the base alignment algorithm, the new version has similar in v2.22 incur little additional computing and do not change the base alignment
performance to older verions. Minimap2 is consistently faster than Winnowmap2 algorithm, the new version has similar performance to older verions. It is
by several times. consistently faster than Winnowmap2 by several times. Our simple heuristics can
be as effective as more complex solutions on real data and may help the
development of future sequence aligners.
\section*{Acknowledgements} \section*{Acknowledgements}
We thank Arang Rhie and Chirag Jain for providing motivating examples where We thank Arang Rhie and Chirag Jain for providing motivating examples where
@ -218,8 +221,6 @@ older minimap2 underperforms.
\paragraph{Funding\textcolon} This work is funded by NHGRI grant R01HG010040. \paragraph{Funding\textcolon} This work is funded by NHGRI grant R01HG010040.
~\\*
\bibliography{minimap2} \bibliography{minimap2}
\end{document} \end{document}