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fix(faq): Update FAQ to reference AR53 marker set.
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aaronmussig committed Mar 31, 2022
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8 changes: 4 additions & 4 deletions pages/faq.vue
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<li>CheckM completeness estimate &gt;50%</li>
<li>CheckM contamination estimate &lt;10%</li>
<li>quality score, defined as completeness - 5*contamination, &gt;50</li>
<li>contain &gt;40% of the bac120 or arc122 marker genes</li>
<li>contain &gt;40% of the bac120 or arc53 marker genes</li>
<li>contain &lt;1000 contigs</li>
<li>have an N50 &gt;5kb</li>
<li>contain &lt;100,000 ambiguous bases</li>
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<template #how-are-the-bacterial-and-archaeal-multiple-sequence-alignments-constructed>
<p> Bacterial and archaeal multiple sequence alignments (MSAs) are formed
from the concatenation of 120 or 122
from the concatenation of 120 or 53
phylogenetically informative markers, respectively. These marker sets are referred to as
bac120 and arc122 for
bac120 and arc53 for
bacterial and archaeal markers, respectively, and are comprised of proteins or protein
domains specified in the
Pfam v27 or TIGRFAMs v15.0 databases. Details on these markers are available for
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<template #how-are-the-bacterial-and-archaeal-reference-trees-inferred>
Bacterial and archaeal reference trees are inferred from the filtered
bac120 and ar122 multiple sequence
bac120 and ar53 multiple sequence
alignments, respectively. Reference trees contain 1 genome per GTDB species cluster. The
bacterial reference
tree is inferred with FastTree v2.1.10 under the WAG model. The archaeal reference tree
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