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genomewalker committed Mar 2, 2024
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Expand Up @@ -13,7 +13,7 @@ A simple tool to process a BAM file and filter references with uneven coverages
&\hspace{15pt}\text{Alignment Score} = \frac{\lambda \times S - \log(K)}{\log(2)} \\
&\hspace{15pt}\text{where:} \\
&\hspace{15pt}S = (\text{Number of matches} \times \text{Match reward}) - (\text{Number of mismatches} \times \text{Mismatch penalty}) \\
&\hspace{35pt} - (\text{Number of gaps} \times \text{Gap open penalty}) - (\text{Gap extensions} \times \text{Gap extension penalty})
&\hspace{36pt} - (\text{Number of gaps} \times \text{Gap open penalty}) - (\text{Gap extensions} \times \text{Gap extension penalty})
\end{align*}
$$

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