roblanf/sarscov2phylo: 14-09-20

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
71379
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 69034
Alignment length:    29903
Total # residues:    2057839570
Smallest:            29018
Largest:             29903
Average length:      29809.1
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 69034
Alignment length:    29903
Total # residues:    2047985731
Smallest:            28922
Largest:             29675
Average length:      29666.3
Average identity:    100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 68844
Alignment length:    29903
Total # residues:    2042358563
Smallest:            28922
Largest:             29675
Average length:      29666.5
Average identity:    100%
//
alignment stats of global alignment after trimming sites that are >50% gaps
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 68844
Alignment length:    29660
Total # residues:    2037002535
Smallest:            28437
Largest:             29660
Average length:      29588.7
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 122241
#leaves:        68826
#dichotomies:   50928
#leaf labels:   68826
#inner labels:  48062
Number of new sequences added this iteration
3035 alignment_names_new.txt

Notable changes to the scripts in this release

• Number of SPR moves reduced from 10 to 2, after some benchmarking to determine whether this was sensible. I'll keep an eye on it, but my analyses suggest that 1 round of SPR moves should be enough to find and fix any large issues in the tree, so 2 is still conservative.

Notable aspects of the trees

• None