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roblanf/sarscov2phylo: 12-10-20

roblanf; Richard Mansfield


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.4089815", 
  "title": "roblanf/sarscov2phylo: 12-10-20", 
  "issued": {
    "date-parts": [
      [
        2020, 
        10, 
        15
      ]
    ]
  }, 
  "abstract": "Citation and reuse\n<p>Please cite this release as:</p>\n<blockquote><p>Lanfear, Rob (2020). A global phylogeny of SARS-CoV-2 sequences from GISAID.  Zenodo DOI: 10.5281/zenodo.3958883</p>\n</blockquote>\n<p>You can visit that DOI here: <a href=\"https://zenodo.org/badge/latestdoi/260124648\"></a></p>\n<p>If you publish papers that use this tree you must still follow the GISAID data sharing and attribution rules.</p>\nDetails\n<p>The trees in this release were generated with the following command line:</p>\n<p><code>bash global_tree_gisaid_start_tree.sh -i [gisaid.fasta] -p [previous_iteration] -t 250</code></p>\n<ul>\n<li><p>[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</p>\n</li>\n<li><p>[previous_iteration] is the filepath of the previous release, this is used to provide the <code>excluded_sequences.tsv</code> and <code>ft_SH.tree</code> files as the starting points of the current iteration.</p>\n</li>\n</ul>\nFiltering statistics\n<pre><code>sequences downloaded from GISAID\n103337\n//\nalignment stats of global alignment\nAlignment number:    1\nFormat:              aligned FASTA\nNumber of sequences: 101866\nAlignment length:    29903\nTotal # residues:    3036101863\nSmallest:            29030\nLargest:             29903\nAverage length:      29804.9\nAverage identity:    100%\n//\nalignment stats of global alignment after masking sites\nAlignment number:    1\nFormat:              aligned FASTA\nNumber of sequences: 101866\nAlignment length:    29903\nTotal # residues:    3022053816\nSmallest:            28961\nLargest:             29675\nAverage length:      29667.0\nAverage identity:    100%\n//\nalignment stats after filtering out short/ambiguous sequences\nAlignment number:    1\nFormat:              aligned FASTA\nNumber of sequences: 101676\nAlignment length:    29903\nTotal # residues:    3016426648\nSmallest:            28961\nLargest:             29675\nAverage length:      29667.0\nAverage identity:    100%\n//\nalignment stats of global alignment after trimming sites that are &gt;50% gaps\nAlignment number:    1\nFormat:              aligned FASTA\nNumber of sequences: 101676\nAlignment length:    29646\nTotal # residues:    3008318632\nSmallest:            28437\nLargest:             29646\nAverage length:      29587.3\nAverage identity:    100%\n//\nAfter filtering sequences with TreeShrink\nType:   Phylogram\n#nodes: 177999\n#leaves:    101609\n#dichotomies:   72563\n#leaf labels:   101609\n#inner labels:  68285\nNumber of new sequences added this iteration\n2604 alignment_names_new.txt\n</code></pre>\nNotable changes to the scripts in this release\n<ul>\n<li>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. </li>\n</ul>\n<p>If you have a GISAID data stream, this means you can get the data as follows:</p>\n<pre><code>curl -u \"${GISAID_LOGIN}:${GISAID_PASSWORD}\" ${URL} 2&gt;/dev/null \\\n    | xz -d -T22 \\\n    | jq -r 'select(.covv_subm_date &lt;= \"'\"$DATE\"'\" and .is_complete == true and .is_high_coverage == true) | [\"&gt;\" + .covv_accession_id + \"\\n\" + .sequence] | join(\"\\n\")' \\\n    | xz -c -T22 &gt; gisaid-${DATE}.fasta.xz\n</code></pre>\nNotable aspects of the trees\n<ul>\n<li>Names have changed to include only the EPI-IDs. This has the side-benefit of roughly halving the size of the tree file.</li>\n</ul>", 
  "author": [
    {
      "family": "roblanf"
    }, 
    {
      "family": "Richard Mansfield"
    }
  ], 
  "version": "12-10-20", 
  "type": "article", 
  "id": "4089815"
}
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