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\title[Long-read and assembly alignment with minimap2]{Minimap2: fast sequence alignment for long noisy reads and assembly contigs}
\author[Li]{Heng Li}
\address{Broad Institute, 415 Main Street, Cambridge, MA 02142, USA}

\maketitle

\begin{abstract}
\section{Summary:} Minimap2 is a program to align long noisy sequences against
a large reference database. It targets query sequences of 1kb--100Mb in length
with sequence divergence typically below 25\%. Minimap2 is $\sim$30 times
faster than most existing long-read aligners and achieves higher accuracy on
simulated data. It also employs concave gap cost and rescues inversions for
improved alignment around potential structural variations.

\section{Availability and implementation:}
\href{https://github.com/lh3/minimap2}{https://github.com/lh3/minimap2}

\section{Contact:} hengli@broadinstitute.org
\end{abstract}

\section{Introduction}

Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore
technologies (ONT) produce reads over 10kbp in length at an error rate
$\sim$15\%. Several aligners have been developed for such
data~\citep{Chaisson:2012aa,Li:2013aa,Liu:2016ab,Sovic:2016aa,Liu:2017aa,Lin:2017aa}.
They are usually five times as slow as mainstream short-read
aligners~\citep{Langmead:2012fk,Li:2013aa}. We speculated there could be
substantial room for speedup on the thought that 10kb long sequences should be
easier to map than 100bp reads because we can more effectively skip repetitive
regions and dramatically reduce computation. We confirmed our speculation by
achieving approximate mapping 50 times faster than BWA-MEM~\citep{Li:2016aa}.
\citet{Suzuki:2016} extended our work with with a fast and novel algorithm on
generating detailed alignment, which in turn inspired us to develop minimap2
towards higher accuracy.

\begin{methods}
\section{Methods}

Minimap2 is the successor of minimap~\citep{Li:2016aa}. It uses similar
indexing and seeding algorithms except that minimap2 optionally uses
homopolymer-compressed (HPC; cite) $k$-mers in addition to normal $k$-mers.
Indexing with HPC $k$-mers leads to higher mapping sensitivity for SMRT reads.
Minimap2 further implements a more accurate chaining algorithm and adds
the ability to produce detailed alignment.

\subsection{Chaining}

\subsubsection{Chaining}
An \emph{anchor} is a 3-tuple $(x,y,w)$, indicating interval $[x-w+1,x]$ on the
reference matching interval $[y-w+1,y]$ on the query. Given a list of anchors
sorted by the ending reference position $x$, let $f(i)$ be the maximal chaining
score up to the $i$-th anchor in the list. $f(i)$ can be calculated with
dynamic programming (DP):
\begin{equation}\label{eq:chain}
f(i)=\max\big\{\max_{i>j\ge 1} \{ f(j)+d(j,i)-\gamma(j,i) \},w_i\big\}
\end{equation}
where $d(j,i)=\min\big\{\min\{y_i-y_j,x_i-x_j\},w_i\big\}$ is the number of
matching bases between the two anchors. $\gamma(j,i)>0$ is the gap cost. It
equals $\infty$ if $y_j\ge y_i$ or $\max\{y_i-y_j,x_i-x_j\}>G$ (i.e. the
distance between two anchors is too large); otherwise
\[
\gamma(j,i)=\gamma'(\max\{y_i-y_j,x_i-x_j\}-\min\{y_i-y_j,x_i-x_j\})
\]
In implementation, a gap of length $l$ costs $\gamma'(l)=\alpha\cdot
l+\beta\log_2(l)$, which is concave. For $m$ anchors, computing all $f(\cdot)$
with Eq.~(\ref{eq:chain}) takes $O(m^2)$ time. We note that if anchor $i$ is
appended to $j$, appending $i$ to a predecessor of $j$ is likely to yield a
lower score. When evaluating Eq.~(\ref{eq:chain}), we start from anchor $i-1$
and stop the evaluation if we cannot find a better $\max$ after up to $h$
iterations. This heuristic reduces the average time to $O(h\cdot m)$. In
practical, we can almost always find the optimal chain with $h=50$; even if the
heuristic fails, the optimal chain often looks dubious.

\subsubsection{Backtracking}
Let $P(i)$ be the index of the best predecessor of anchor $i$. It equals 0 if
$f(i)=w_i$ or $\argmax_j\{f(j)+\eta(j,i)-\gamma(j,i)\}$ otherwise. For each
anchor $i$ in the descending order of $f(i)$, we mark $i$ as `used' and apply
$P(\cdot)$ repeatedly to find its predecessor. This process stops at $P(j)=0$
or at a `used' $j$. This way we find all chains with no anchors used in
more than one chains.

\subsection{Alignment}
Minimap2 performs DP to align sequences between adjacent anchors in a chain. It
adopted difference-based formulation to derive
alignment~\citep{Wu:1996aa,Suzuki:2016}. When combined with SSE vectorization,
this formulation has two advantages. First, because each score in the DP matrix
is bounded by the gap cost and the maximum matching score, we can usually
achieve 16-way SSE vectorization regardless of the peak score of the
alignment. Second, filling the DP matrix along the diagonal, we can simplify
banded alignment, which is critical to performance. In practice, our
implementation is three times as fast as Parasail's 4-way
vectorization~\citep{Daily:2016aa} for global alignment.


Minimap2 uses a 2-piece affine gap cost~\citep{Gotoh:1990aa}:
\[
\gamma(l)=\min\{q+l\cdot e,\tilde{q}+l\cdot\tilde{e}\}
\]
On the condition that $q+e<\tilde{q}+\tilde{e}$ and $e>\tilde{e}$, this
cost function is concave. It applies cost $q+l\cdot e$ to gaps shorter than
$\lceil(\tilde{q}-q)/(e-\tilde{e})\rceil$ and applies
$\tilde{q}+l\cdot\tilde{e}$ to longer gaps. This scheme helps to recover
longer insertions and deletions.

%\begin{equation}\label{eq:ae86}
%\left\{\begin{array}{l}
%H_{ij} = \max\{H_{i-1,j-1}+s(i,j),E_{ij},F_{ij},\tilde{E}_{ij},\tilde{F}_{ij}\}\\
%E_{i+1,j}= \max\{H_{ij}-q,E_{ij}\}-e\\
%F_{i,j+1}= \max\{H_{ij}-q,F_{ij}\}-e\\
%\tilde{E}_{i+1,j}= \max\{H_{ij}-\tilde{q},\tilde{E}_{ij}\}-\tilde{e}\\
%\tilde{F}_{i,j+1}= \max\{H_{ij}-\tilde{q},\tilde{F}_{ij}\}-\tilde{e}
%\end{array}\right.
%\end{equation}
%where $s(i,j)$ is the score between the $i$-th reference base and $j$-th query
%base. If we define~\citep{Wu:1996aa,Suzuki:2016}
%\[
%\left\{\begin{array}{ll}
%u_{ij}\triangleq H_{ij}-H_{i-1,j} & v_{ij}\triangleq H_{ij}-H_{i,j-1} \\
%x_{ij}\triangleq E_{i+1,j}-H_{ij} & \tilde{x}_{ij}\triangleq \tilde{E}_{i+1,j}-\tilde{H}_{ij} \\
%y_{ij}\triangleq F_{i,j+1}-H_{ij} & \tilde{y}_{ij}\triangleq \tilde{F}_{i,j+1}-\tilde{H}_{ij}
%\end{array}\right.
%\]
%we can transform Eq.~(\ref{eq:ae86}) to
%\[
%\left\{\begin{array}{lll}
%z_{ij}&=&\max\{s(i,j),x_{i-1,j}+v_{i-1,j},y_{i,j-1}+u_{i,j-1},\\
%&&\tilde{x}_{i-1,j}+v_{i-1,j},\tilde{y}_{i,j-1}+u_{i,j-1}\}\\
%u_{ij}&=&z_{ij}-v_{i-1,j}\\
%v_{ij}&=&z_{ij}-u_{i,j-1}\\
%x_{ij}&=&\max\{0,x_{i-1,j}+v_{i-1,j}-z_{ij}+q\}-q-e\\
%y_{ij}&=&\max\{0,y_{i,j-1}+u_{i,j-1}-z_{ij}+q\}-q-e\\
%\tilde{x}_{ij}&=&\max\{0,\tilde{x}_{i-1,j}+v_{i-1,j}-z_{ij}+\tilde{q}\}-\tilde{q}-\tilde{e}\\
%\tilde{y}_{ij}&=&\max\{0,\tilde{y}_{i,j-1}+u_{i,j-1}-z_{ij}+\tilde{q}\}-\tilde{q}-\tilde{e}
%\end{array}\right.
%\]
%with boundary conditions
%\[
%\left\{\begin{array}{l}
%x_{-1,\cdot}=y_{\cdot,-1}=-q-e\\
%\tilde{x}_{-1,\cdot}=\tilde{y}_{\cdot,-1}=-\tilde{q}-\tilde{e}\\
%u_{i,-1}=\eta(i)\\
%v_{-1,j}=\eta(j)
%\end{array}\right.
%\]
%where
%\[
%\eta(k)=\left\{\begin{array}{ll}
%-q-e & (k=0) \\
%-e & (k<\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil) \\
%i\cdot(e-\tilde{e})-(\tilde{q}-q)-\tilde{e} & (k=\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil) \\
%-\tilde{e} & (k>\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil)
%\end{array}\right.
%\]

\end{methods}

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