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roblanf/sarscov2phylo: 3-11-20

roblanf; Richard Mansfield


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    <dct:title>roblanf/sarscov2phylo: 3-11-20</dct:title>
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    <dct:description>Citation and reuse &lt;p&gt;Please cite this release as:&lt;/p&gt; &lt;blockquote&gt;&lt;p&gt;Lanfear, Rob (2020). A global phylogeny of SARS-CoV-2 sequences from GISAID. Zenodo DOI: 10.5281/zenodo.3958883&lt;/p&gt; &lt;/blockquote&gt; &lt;p&gt;You can visit that DOI here: &lt;a href="https://zenodo.org/badge/latestdoi/260124648"&gt;&lt;/a&gt;&lt;/p&gt; &lt;p&gt;If you publish papers that use this tree you must still follow the GISAID data sharing and attribution rules.&lt;/p&gt; Details &lt;p&gt;The trees in this release were generated with the following command line:&lt;/p&gt; &lt;p&gt;&lt;code&gt;bash global_tree_gisaid_start_tree.sh -i [gisaid.fasta] -p [previous_iteration] -t 250&lt;/code&gt;&lt;/p&gt; &lt;ul&gt; &lt;li&gt;&lt;p&gt;[gisaid.fasta] is the fasta file of high coverage and complete raw sequences from GISAID up to and including the date in the title of the release, determined by the 'submission date' filter on a GISAID data feed&lt;/p&gt; &lt;/li&gt; &lt;li&gt;&lt;p&gt;[previous_iteration] is the filepath of the previous release, this is used to provide the &lt;code&gt;excluded_sequences.tsv&lt;/code&gt; and &lt;code&gt;ft_SH.tree&lt;/code&gt; files as the starting points of the current iteration.&lt;/p&gt; &lt;/li&gt; &lt;/ul&gt; Filtering statistics &lt;pre&gt;&lt;code&gt;sequences downloaded from GISAID 131215 // alignment stats of global alignment Alignment number: 1 Format: aligned FASTA Number of sequences: 128821 Alignment length: 29903 Total # residues: 3839063069 Smallest: 29105 Largest: 29903 Average length: 29801.5 Average identity: 100% // alignment stats of global alignment after masking sites Alignment number: 1 Format: aligned FASTA Number of sequences: 128821 Alignment length: 29903 Total # residues: 3821789644 Smallest: 29036 Largest: 29675 Average length: 29667.4 Average identity: 100% // alignment stats after filtering out short/ambiguous sequences Alignment number: 1 Format: aligned FASTA Number of sequences: 128777 Alignment length: 29903 Total # residues: 3820487101 Smallest: 29036 Largest: 29675 Average length: 29667.5 Average identity: 100% // alignment stats of global alignment after trimming sites that are &amp;gt;50% gaps Alignment number: 1 Format: aligned FASTA Number of sequences: 128777 Alignment length: 29646 Total # residues: 3810742331 Smallest: 28498 Largest: 29646 Average length: 29591.8 Average identity: 100% // After filtering sequences with TreeShrink Type: Phylogram #nodes: 224247 #leaves: 128714 #dichotomies: 90656 #leaf labels: 128714 #inner labels: 85123 Number of new sequences added this iteration 6018 alignment_names_new.txt &lt;/code&gt;&lt;/pre&gt; Notable changes to the scripts in this release &lt;ul&gt; &lt;li&gt;None&lt;/li&gt; &lt;/ul&gt; Notable aspects of the trees &lt;ul&gt; &lt;li&gt;There is some notable lack of clustering in some pangolin lineages, but I have not yet had a chance to figure out whether this is an issue with my recently added QC code (quite possible), the tree, or something else.&lt;/li&gt; &lt;/ul&gt;</dct:description>
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