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roblanf/sarscov2phylo: 12-10-20

roblanf; Richard Mansfield


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    <dct:title>roblanf/sarscov2phylo: 12-10-20</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 103337 // alignment stats of global alignment Alignment number: 1 Format: aligned FASTA Number of sequences: 101866 Alignment length: 29903 Total # residues: 3036101863 Smallest: 29030 Largest: 29903 Average length: 29804.9 Average identity: 100% // alignment stats of global alignment after masking sites Alignment number: 1 Format: aligned FASTA Number of sequences: 101866 Alignment length: 29903 Total # residues: 3022053816 Smallest: 28961 Largest: 29675 Average length: 29667.0 Average identity: 100% // alignment stats after filtering out short/ambiguous sequences Alignment number: 1 Format: aligned FASTA Number of sequences: 101676 Alignment length: 29903 Total # residues: 3016426648 Smallest: 28961 Largest: 29675 Average length: 29667.0 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: 101676 Alignment length: 29646 Total # residues: 3008318632 Smallest: 28437 Largest: 29646 Average length: 29587.3 Average identity: 100% // After filtering sequences with TreeShrink Type: Phylogram #nodes: 177999 #leaves: 101609 #dichotomies: 72563 #leaf labels: 101609 #inner labels: 68285 Number of new sequences added this iteration 2604 alignment_names_new.txt &lt;/code&gt;&lt;/pre&gt; Notable changes to the scripts in this release &lt;ul&gt; &lt;li&gt;Some more issues occurred with sequence names, so I have shifted to using exclusively just the EPI-IDs for sequence names in the alignments, trees, and scripts. This should avoid any future issues with sequence names. &lt;/li&gt; &lt;/ul&gt; &lt;p&gt;If you have a GISAID data stream, this means you can get the data as follows:&lt;/p&gt; &lt;pre&gt;&lt;code&gt;curl -u "${GISAID_LOGIN}:${GISAID_PASSWORD}" ${URL} 2&amp;gt;/dev/null \ | xz -d -T22 \ | jq -r 'select(.covv_subm_date &amp;lt;= "'"$DATE"'" and .is_complete == true and .is_high_coverage == true) | ["&amp;gt;" + .covv_accession_id + "\n" + .sequence] | join("\n")' \ | xz -c -T22 &amp;gt; gisaid-${DATE}.fasta.xz &lt;/code&gt;&lt;/pre&gt; Notable aspects of the trees &lt;ul&gt; &lt;li&gt;Names have changed to include only the EPI-IDs. This has the side-benefit of roughly halving the size of the tree file.&lt;/li&gt; &lt;/ul&gt;</dct:description>
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