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roblanf/sarscov2phylo: 3-11-20

roblanf; Richard Mansfield

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
131215
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 128821
Alignment length:    29903
Total # residues:    3839063069
Smallest:            29105
Largest:             29903
Average length:      29801.5
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 128821
Alignment length:    29903
Total # residues:    3821789644
Smallest:            29036
Largest:             29675
Average length:      29667.4
Average identity:    100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 128777
Alignment length:    29903
Total # residues:    3820487101
Smallest:            29036
Largest:             29675
Average length:      29667.5
Average identity:    100%
//
alignment stats of global alignment after trimming sites that are >50% gaps
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 128777
Alignment length:    29646
Total # residues:    3810742331
Smallest:            28498
Largest:             29646
Average length:      29591.8
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 224247
#leaves:    128714
#dichotomies:   90656
#leaf labels:   128714
#inner labels:  85123
Number of new sequences added this iteration
6018 alignment_names_new.txt
Notable changes to the scripts in this release
  • None
Notable aspects of the trees
  • There is some notable lack of clustering in some pangolin lineages, but I have not yet had a chance to figure out whether this is an issue with my recently added QC code (quite possible), the tree, or something else.

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