AppendixA.tex

\addcontentsline{toc}{chapter}{Appendix A -- Software and Scripts}
\chapter*{Appendix A -- Software and Scripts}

The source codes of used software and scripts can be found at GitHub:
\begin{itemize}
\item Scripts that were used to generate the experimental data and figures: \url{https://github.com/maaario/bachelor-thesis-scripts}
\item Our modified version of Kmerlight software: \url{https://github.com/maaario/kmerlight} .
The most important modification, the new method of selecting the level $w^+$, is implemented in
function \texttt{computeFJ\_modified} in the file \\ \texttt{src/CountSketchInstance.h}.

The original version of Kmerlight can be downloaded from \url{https://github.com/nsivad/kmerlight}.

\item CovEst software \cite{Hozza2015} can be downloaded from \url{https://github.com/mhozza/covest}.
Apart from using CovEst to compute coverage estimates, we also used scripts from 
the folder \texttt{tools/simulator} to generate simulated genomes and reads.
\end{itemize}