From 295874ea3023f34cfd06acccfbcf3a3840686906 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 3 Aug 2017 12:17:58 -0400 Subject: [PATCH] spell check --- tex/minimap2.tex | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tex/minimap2.tex b/tex/minimap2.tex index 2be115a..6d121c7 100644 --- a/tex/minimap2.tex +++ b/tex/minimap2.tex @@ -86,8 +86,8 @@ l+\beta\log_2(l)$. For $m$ anchors, directly computing all $f(\cdot)$ with Eq.~(\ref{eq:chain}) takes $O(m^2)$ time. Although theoretically faster chaining algorithms exist~\citep{Abouelhoda:2005aa}, they are inapplicable to generic gap cost, complex to implement and usually -associated with a large constant. We introduced a simple heurstic to accelerate -chaining. +associated with a large constant. We introduced a simple heuristic to +accelerate chaining. 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}), @@ -153,7 +153,7 @@ $j'Z+e\cdot(\max\{i-i',j-j'\}-\min\{i-i',j-j'\}) \] -where $e$ is the gap extension penalty and $Z$ is an aribitrary threshold. +where $e$ is the gap extension penalty and $Z$ is an arbitrary threshold. This strategy is similar to X-drop employed in BLAST~\citep{Altschul:1997vn}. However, unlike X-drop, it would not break the alignment in the presence of a single long gap. @@ -191,7 +191,7 @@ crashed or produced malformatted SAM. In this evaluation, Minimap2 has a higher power to distinguish unique and repetitive hits, and achieves overall higher mapping accuracy (Fig.~\ref{fig:eval}a). It is still the most accurate even if we skip DP-based alignment (data not shown), suggesting chaining alone -is sufficient to achieve high accuracy for approaximate mapping. Minimap2 and +is sufficient to achieve high accuracy for approximate mapping. Minimap2 and NGMLR provide better mapping quality estimate: they rarely give repetitive hits high mapping quality (Fig.~\ref{fig:eval}b). Apparently, other aligners may occasionally miss close suboptimal hits and be overconfident in wrong mappings. @@ -221,7 +221,7 @@ In addition to reference-based read mapping, minimap2 inherits minimap's ability to search against huge multi-species data and to find read overlaps. On a few test data sets, minimap2 appears to yield slightly better miniasm assembly. Minimap2 can also align long assemblies or closely related genomes, -though more thorough evaluation is needed. Genome alignment is an intricate +though more thorough evaluations are needed. Genome alignment is an intricate topic. \section*{Acknowledgements}