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1 parent 8aab977 commit debebc9bebd05af1f77611b009ee0ceb8bed3612 @ctb ctb committed Oct 25, 2012
Showing with 6 additions and 6 deletions.
  1. +6 −6 recent-version/artifacts-paper2.tex
@@ -397,7 +397,7 @@ \subsection*{Sequencing artifacts are present in highly connected sequences}
diversity and very low coverage of these soil samples, the magnitude of the
observed increases in connectivity are unlikely to be due to increased
coverage. This further suggests the presence of sequencing artifacts
-that falsely increas connectivity.
+that falsely increase connectivity.
The superlinear increase in connectivity exhibited in these data sets
suggests that a form of preferential attachment is occurring in the
@@ -413,7 +413,7 @@ \subsection*{Sequencing artifacts are present in highly connected sequences}
specific but random subsequences.
% @CTB talk about general delumping coolness; general approaches to finding
-% and characteristing graph connectivity.
+% and characterizing graph connectivity.
We believe a significant component of the high connectivity that we
see is of non-biological origin. Shotgun sequencing is a random
@@ -567,7 +567,7 @@ \subsection*{Highly connected sequences do not match known reference sequences}
with the identification of conserved biological motifs in the
simulated dataset which would result in a small number of highly
abundant sequences. In contrast, within metagenomic data, we found
-that the 5-mersse are evenly distributed and random in metagenomes
+that the 5-mers are evenly distributed and random in metagenomes
(Figure 5), making them difficult to identify and evaluate.
\section*{Conclusion}
@@ -752,7 +752,7 @@ \subsection*{\emph{De novo} metagenomic assembly}
\caption{The original size and proportion of highly connective 32-mers in the largest subset of partitioned reads (``lump'') in several medium to high complexity metagenomes. Read coverage was estimated with the number of aligned sequencing reads to Velvet-assembled contigs (K=33). The dominant lump, or largest disconnected component of each metagenome assembly graph, was found to contain highly connecting k-mers responsible for high local graph density.}
\begin{tabular}{lp{2cm}cp{2cm}cp{2cm}cp{2cm}cp{2cm}cp{2cm}cp{2cm}cp{2cm}cp{2cm}|}
\hline
-& Reads & Mapped to assebmly & Lump reads & Highly connective & Total & Highly connective & Density \textgreater 20 \\
+& Reads & Mapped to assembly & Lump reads & Highly connective & Total & Highly connective & Density \textgreater 20 \\
& (millions) & (percent) & (millions) & (32-mers) & (32-mers) & (percent) & (percent) \\
\hline
@@ -844,7 +844,7 @@ \subsection*{\emph{De novo} metagenomic assembly}
\end{tabular}
\begin{tabular}{*{4}{p{5cm}}}
\hline
-SOAPdeNOVO Assembler \\
+SOAPdenovo Assembler \\
\hline
Small Soil &14,275 / 7,100,052 / 37,720 &12,801 / 6,343,110 / 13,246 &3 / \textless1\\
Medium Soil &66,640 / 33,321,411 / 28,695 &56,023 / 27,880,293 / 15,721 &10 / \textless1\\
@@ -872,7 +872,7 @@ \subsection*{\emph{De novo} metagenomic assembly}
Diguanylate cyclase/phosphodiesterase &36\\
ATPase &36\\
S-adenosyl-L-homocysteine hydrolase &36\\
-AdensylhoMocysteine And downstream NAD binding &36\\
+Adenosylhomocysteine And downstream NAD binding &36\\
Ketol-acid reductoisomerase &34\\
S-adenosylmethionine synthetase &34\\
Elongation factor G &34\\

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