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@ -480,7 +480,7 @@ applications, but it has to apply different sets of parameters depending on
input data types. Similar to BWA-MEM, minimap2 introduces `presets' that input data types. Similar to BWA-MEM, minimap2 introduces `presets' that
modify multiple parameters with a simple invokation. Detailed settings modify multiple parameters with a simple invokation. Detailed settings
and command-line options can be found in the minimap2 manpage. In addition to and command-line options can be found in the minimap2 manpage. In addition to
the applications described in the following sections, minimap2 also retains the applications evaluated in the following sections, minimap2 also retains
minimap's functionality to find overlaps between long reads and to search minimap's functionality to find overlaps between long reads and to search
against large multi-species databases such as \emph{nt} from NCBI. against large multi-species databases such as \emph{nt} from NCBI.
@ -654,22 +654,22 @@ context of small variant calling.
\subsection{Aligning long-read assemblies} \subsection{Aligning long-read assemblies}
Minimap2 can align a human SMRT assembly (AC:GCA\_001297185.1) against Minimap2 can align a SMRT assembly (AC:GCA\_001297185.1) against GRCh38 in 7
GRCh38 in 7 minutes using 8 CPU cores, over 20 times faster than minutes using 8 CPU cores, over 20 times faster than nucmer from
MUMmer4~\citep{Marcais:2018aa}. With the paftools.js script from the minimap2 MUMmer4~\citep{Marcais:2018aa}. With the paftools.js script from the minimap2
package, we called 2.67 million single-base substitutions out of 2.78Gbp package, we called 2.67 million single-base substitutions out of 2.78Gbp
genomic regions. The transition-to-transversion ratio (ts/tv) is 2.01. In genomic regions. The transition-to-transversion ratio (ts/tv) is 2.01. In
comparison, using MUMmer4's dnadiff pipeline, we called 2.86 million comparison, using MUMmer4's dnadiff pipeline, we called 2.86 million
substitutions in 2.83Gbp at ts/tv=1.87. Given that ts/tv averaged across the substitutions in 2.83Gbp at ts/tv=1.87. Given that ts/tv averaged across the
human genome is about 2 but ts/tv averaged over random errors is 0.5, the human genome is about 2 but ts/tv averaged over random errors is 0.5, the
minimap2 callset arguably has higher accuracy. minimap2 callset arguably has higher precision at lower sensitivity.
The sample being assembled is a female. Minimap2 still called 201 substitutions The sample being assembled is a female. Minimap2 still called 201 substitutions
on the Y chromosome. These substitutions all come from one contig aligned at on the Y chromosome. These substitutions all come from one contig aligned at
96.8\% sequence identity. The contig could be a diverged segmental duplication 96.8\% sequence identity. The contig could be a segmental duplication
absent from GRCh38. In constrast, on the Y chromosome, MUMmer4 called 9070 absent from GRCh38. In constrast, dnadiff called 9070 substitutions on the Y
substitutions across 73 SMRT contigs. The accuracy of the MUMmer4 pipeline is chromosome across 73 SMRT contigs. This again implies our minimap2-based
probably lower than our minimap2-based pipeline. pipeline has higher precision.
\section{Discussions} \section{Discussions}