feat(methods): Update reference to AR53 instead of AR122.

Ecogenomics · Mar 29, 2022 · 7bd5b93 · 7bd5b93
1 parent 2f1f71b
commit 7bd5b93
Showing 1 changed file with 8 additions and 3 deletions.
diff --git a/pages/methods.vue b/pages/methods.vue
@@ -30,8 +30,9 @@
         </p>
         <p class="mb-0">
           Archaea reference tree is inferred with IQ-Tree v1.6.9 under the PMSF model
-          from the concatenated alignment of 122 ubiquitous archaeal genes
-          <a href="https://doi.org/10.1038/nbt.4229" target="_blank">(Parks et al., 2018)</a>,
+          from the concatenated alignment of 53 archaeal genes based on a subset of the "top-ranked marker proteins"
+          from a recent evaluation based on minimizing horizontal gene transfer and optimising the recovery of monophyletic lineages
+          <a href="https://doi.org/10.1038/s41467-020-17408-w" target="_blank">(Rinke & Spang et al., 2020)</a>,
           using FastTree v2.1.10 to infer an initial guide tree.
         </p>
       </template>
@@ -62,7 +63,7 @@
           <li>CheckM completeness estimate >50%</li>
           <li>CheckM contamination estimate <10%</li>
           <li>quality score, defined as completeness - 5*contamination, >50</li>
-          <li>contain >40% of the bac120 or arc122 marker genes</li>
+          <li>contain >40% of the bac120 or arc53 marker genes</li>
           <li>contain <1000 contigs</li>
           <li>have an N50 >5kb</li>
           <li>contain <100,000 ambiguous bases</li>
@@ -169,6 +170,10 @@
               <td>Full length 16S rRNA gene</td>
               <td>10</td>
             </tr>
+            <tr>
+              <td>Many frameshifted proteins according to NCBI</td>
+              <td>-25</td>
+            </tr>
             </tbody>
           </template>
         </v-simple-table>