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28-08-20

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@roblanf roblanf released this 02 Sep 04:32
· 96 commits to master since this release

Citation and reuse

Please cite this release as:

Lanfear, Rob (2020). A global phylogeny of SARS-CoV-2 from GISAID data, including sequences deposited up to 28-August-2020. Zenodo DOI: 10.5281/zenodo.3958883

You can visit that DOI here: DOI

Please note - you cannot publish papers that use this tree without following the GISAID data sharing and attribution rules. These rules are important - they protect the data uploaders, and create trust in a global system of data sharing with potentially vast public health benefits. By building and maintaining trust we ensure that people keep sharing their data, and that the public health benefits keep flowing. I do not want the existence of this tree to be some kind of attribution laundering service (e.g. where people feel free to use the tree without following the GISAID data sharing rules), so please don't use it in that way. For example, if you are going to interpret other people's data from GISAID and publish the results, including by using this tree, you should get in touch with the people that submitted the data. The code in this repo is covered by the GNU license, and you can use that however you like.

Details

The trees in this release were generated with the following command line:

bash global_tree_gisaid_start_tree.sh -i gisaid_hcov-19_2020_08_31_23.fasta -o global.fa -s ft_SH_26-08-20.tree -t 250

The raw sequence file contains all available SARS-CoV-2 genomes in GISAID available on the 28th of August 2020, determined by the 'submission date' filter on GISAID.

The ZIP file contains the code necessary to reproduce the trees themselves, and the README in the zip file also describes the methods used in detail. I also include the tree itself here so that it can be easily downloaded without downloading the entire repo. The file ' ft_SH_26-8-20.tree' is the 'ft_SH.tree' file from the 26-8-20 release.

The lnL of the final tree is: -564605.798

Filtering statistics

sequences downloaded from GISAID
61880
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 59889
Alignment length:    29903
Total # residues:    1786554388
Smallest:            29018
Largest:             29903
Average length:      29831.1
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 59889
Alignment length:    29903
Total # residues:    1776728654
Smallest:            28922
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: 59612
Alignment length:    29903
Total # residues:    1768521884
Smallest:            28922
Largest:             29675
Average length:      29667.2
Average identity:    100%
//
alignment stats of global alignment after trimming sites that are >50% gaps
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 59612
Alignment length:    29661
Total # residues:    1764399545
Smallest:            28437
Largest:             29661
Average length:      29598.1
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 105877
#leaves:        59600
#dichotomies:   44150
#leaf labels:   59600
#inner labels:  41689
Number of new sequences added this iteration
1097 alignment_names_new.txt

Notable changes to the scripts in this release

  • None

Notable aspects of the trees

  • None