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Title: roblanf/sarscov2phylo: 06-09-20

Type Software roblanf, Richard Mansfield (2020): roblanf/sarscov2phylo: 06-09-20. Zenodo. Software. https://zenodo.org/record/4037307

Authors: roblanf ; Richard Mansfield ;

Links

Summary

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 GISAID

[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 66966 // alignment stats of global alignment Alignment number: 1 Format: aligned FASTA Number of sequences: 64801 Alignment length: 29903 Total # residues: 1931706492 Smallest: 29018 Largest: 29903 Average length: 29809.8 Average identity: 100% // alignment stats of global alignment after masking sites Alignment number: 1 Format: aligned FASTA Number of sequences: 64801 Alignment length: 29903 Total # residues: 1922380482 Smallest: 28922 Largest: 29675 Average length: 29665.9 Average identity: 100% // alignment stats after filtering out short/ambiguous sequences Alignment number: 1 Format: aligned FASTA Number of sequences: 64613 Alignment length: 29903 Total # residues: 1916812664 Smallest: 28922 Largest: 29675 Average length: 29666.1 Average identity: 100% // alignment stats of global alignment after trimming sites that are >50% gaps Alignment number: 1 Format: aligned FASTA Number of sequences: 64613 Alignment length: 29661 Total # residues: 1911717961 Smallest: 28437 Largest: 29661 Average length: 29587.2 Average identity: 100% // After filtering sequences with TreeShrink Type: Phylogram #nodes: 114973 #leaves: 64606 #dichotomies: 48085 #leaf labels: 64606 #inner labels: 45419 Number of new sequences added this iteration 390 alignment_names_new.txt Notable changes to the scripts in this release None Notable aspects of the trees None

More information

  • DOI: 10.5281/zenodo.4037307

Dates

  • Publication date: 2020
  • Issued: September 18, 2020

Rights

  • info:eu-repo/semantics/openAccess Open Access

Much of the data past this point we don't have good examples of yet. Please share in #rdi slack if you have good examples for anything that appears below. Thanks!

Format

electronic resource

Relateditems

DescriptionItem typeRelationshipUri
IsSupplementTohttps://github.com/roblanf/sarscov2phylo/tree/06-09-20
IsVersionOfhttps://doi.org/10.5281/zenodo.3958883
IsPartOfhttps://zenodo.org/communities/covid-19
IsPartOfhttps://zenodo.org/communities/zenodo