There is a 较新的版本 这个记录可用。

软件 开放访问

Roblanf / Sarscov2phylo:22-10-20

roblanf. ; 理查德曼斯菲尔德


都柏林核心出口

<?xml version='1.0' encoding='utf-8'?>
<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>roblanf</dc:creator>
  <dc:creator>Richard Mansfield</dc:creator>
  <dc:date>2020-10-30</dc:date>
  <dc:description>Citation and reuse
Please cite this release as:
Lanfear, Rob (2020). A global phylogeny of SARS-CoV-2 sequences from GISAID.  Zenodo DOI: 10.5281 / zenodo.3958883

You can visit that DOI here: 
If you publish papers that use this tree you must still follow the GISAID data sharing and attribution rules.
Details
The trees in this release were generated with the following command line:
bash global_tree_gisaid_start_tree.sh -i [gisaid.fasta] -p [previous_iteration] -t 250

[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

[previous_iteration] is the filepath of the previous release, this is used to provide the excluded_sequences.tsv and ft_SH.tree files as the starting points of the current iteration.


Filtering statistics
sequences downloaded from GISAID
115519
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 113661
Alignment length:    29903
Total # residues:    3387462587
Smallest:            29030
Largest:             29903
Average length:      29803.2
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 113661
Alignment length:    29903
Total # residues:    3372017748
Smallest:            28961
Largest:             29675
Average length:      29667.3
Average identity:    100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 113470
Alignment length:    29903
Total # residues:    3366361022
Smallest:            28961
Largest:             29675
Average length:      29667.4
Average identity:    100%
//
alignment stats of global alignment after trimming sites that are &gt;50% gaps
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 113470
Alignment length:    29646
Total # residues:    3357452880
Smallest:            28437
Largest:             29646
Average length:      29588.9
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 198338
#leaves:    113377
#dichotomies:   80691
#leaf labels:   113377
#inner labels:  75842
Number of new sequences added this iteration
1773 alignment_names_new.txt

Notable changes to the scripts in this release

Scripts have changed to include some simple QC.

Notable aspects of the trees

None
</dc:description>
  <dc:identifier>//americinnmankato.com/record/4162150</dc:identifier>
  <dc:identifier>10.5281 / zenodo.4162150</dc:identifier>
  <dc:identifier>oai:zenodo.org:4162150</dc:identifier>
  <dc:relation>url://github.com/roblanf/sarscov2phylo/tree/22-10-20</dc:relation>
  <dc:relation>doi:10.5281 / zenodo.3958883</dc:relation>
  <dc:relation>url://americinnmankato.com/communities/covid-19</dc:relation>
  <dc:relation>url://americinnmankato.com/communities/zenodo</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:title>Roblanf / Sarscov2phylo:22-10-20</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>
7,212
379
views
downloads
所有版本 这个版本
意见 7,21281
下载 37912
数据量 3.4 GB 118.6 MB.
独特的观点 5,76447
独特的下载 32011

分享

引用