Update README.md

README.md

@@ -6,18 +6,16 @@ Perform hard selective masking of ancient DNA deamination patterns, using the ou
 
 # Preface
 
-`pmd-mask` is a simple preprocessing and quality filtration command-line utility designed to selectively mask potentially deaminated nucleotides within ancient DNA alignement files, changing putative deaminated bases to ‘N’ and quality to ‘!’.
-
-This method may be regarded as a conservative compromise between post-morterm damage rescaling methods such as [MapDamage](https://ginolhac.github.io/mapDamage/) or [PMDtools](/~https://github.com/pontussk/PMDtools), and hard-clipping methods such as [`bamUtils trimBam`]. Here, `pmd-mask` instead leverages nucleotide and position specific misincorporation rate estimes emitted from [MapDamage](https://ginolhac.github.io/mapDamage/) to selectively trim read ends, up-until the local misincorporation rate reaches a designated, user-defined threshold (default: 1%). This approach can thus greatly mitigate the loss of information usually displayed when applying hard-clipping on ancient DNA samples, by *specifically* targeting potential `C>T` and `G>A` transitions on both the 5’ and 3’ end of the read, respectively.
+`pmd-mask` is a simple preprocessing and quality filtration command-line utility designed to selectively mask potentially deaminated nucleotides within ancient DNA alignement files, changing putative deaminated bases to `N` and quality to `!`.
 
+This method may be regarded as a conservative compromise between post-morterm damage rescaling methods such as [`MapDamage`](https://ginolhac.github.io/mapDamage/) or [`PMDtools`](/~https://github.com/pontussk/PMDtools), and hard-clipping methods such as the [`trimBam`](https://genome.sph.umich.edu/wiki/BamUtil:_trimBam) module of [`bamUtil`](/~https://github.com/statgen/bamUtil). Here, `pmd-mask` instead leverages nucleotide and position specific misincorporation rate estimes emitted from [`MapDamage`](https://ginolhac.github.io/mapDamage/) to selectively trim read ends, up-until the local misincorporation rate reaches a designated, user-defined threshold (default: 1%). This approach can thus greatly mitigate the loss of information usually displayed when applying hard-clipping on ancient DNA samples, by *specifically* targeting potential `C>T` and `G>A` transitions on both the `5’` and `3’` end of the read, respectively.
 
 <p align="center">
-  <figure align="center">
-    <img src="docs/images/preface-illustration.png" alt="An illustration of how pmd-mask operates" title="This is a Title"> 
-    <figcaption>
+  <img src="docs/images/preface-illustration.png" alt="An illustration of how pmd-mask operates" title="This is a Title">
+  <br>
+  <caption>
       <em>Figure 1.</em> An illustration of how pmd-mask operates. 
-    </figcaption>
-  </figure>
+  </caption>
 </p>