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罗布兰夫 / sarscov2phylo:20年5月11日

罗布兰夫; 理查德·曼斯菲尔德


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<?xml version='1.0' encoding='utf-8'?>
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  <identifier identifierType="DOI">10.5281 / zenodo.4289376</identifier>
  <creators>
    <creator>
      <creatorName>roblanf</creatorName>
    </creator>
    <creator>
      <creatorName>Richard Mansfield</creatorName>
    </creator>
  </creators>
  <titles>
    <title>roblanf / sarscov2phylo:20年5月11日</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <dates>
    <date dateType="Issued">2020-11-24</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">//americinnmankato.com/record/4289376</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">//github.com/roblanf/sarscov2phylo/tree/5-11-20</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281 / zenodo.3958883</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">//americinnmankato.com/communities/covid-19</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">//americinnmankato.com/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>5-11-20</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">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 土井: 10.5281 / zenodo.3958883&lt;/p&gt;
&lt;/blockquote&gt;
&lt;p&gt;You can visit that 土井 here: &lt;a href="//americinnmankato.com/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
136871
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 134414
Alignment length:    29903
Total # residues:    4005663633
Smallest:            29105
Largest:             29903
Average length:      29800.9
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 134414
Alignment length:    29903
Total # residues:    3987748459
Smallest:            29036
Largest:             29675
Average length:      29667.7
Average identity:    100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 134370
Alignment length:    29903
Total # residues:    3986445916
Smallest:            29036
Largest:             29675
Average length:      29667.7
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: 134370
Alignment length:    29646
Total # residues:    3976491642
Smallest:            28498
Largest:             29646
Average length:      29593.6
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 233128
#leaves:    134252
#dichotomies:   93693
#leaf labels:   134252
#inner labels:  87918
Number of new sequences added this iteration
5656 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;None&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
</resource>
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