From 8e81145817954fd709884ba4abcfffc9ed1cd957 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 7 Aug 2021 00:33:31 -0400 Subject: [PATCH] finished the first draft --- tex/mm2-update.tex | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/tex/mm2-update.tex b/tex/mm2-update.tex index 8566e9d..cd27711 100644 --- a/tex/mm2-update.tex +++ b/tex/mm2-update.tex @@ -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 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 -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. 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. 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 -performance to older verions. Minimap2 is consistently faster than Winnowmap2 -by several times. - +in v2.22 incur little additional computing and do not change the base alignment +algorithm, the new version has similar performance to older verions. It is +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} 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. -~\\* - \bibliography{minimap2} \end{document}