roblanf/sarscov2phylo: 30-08-20

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.

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.

sequences downloaded from GISAID
61969
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 59968
Alignment length:    29903
Total # residues:    1788904459
Smallest:            29018
Largest:             29903
Average length:      29831.0
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 59968
Alignment length:    29903
Total # residues:    1779071662
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: 59692
Alignment length:    29903
Total # residues:    1770894567
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: 59692
Alignment length:    29661
Total # residues:    1766765393
Smallest:            28437
Largest:             29661
Average length:      29598.0
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 106041
#leaves:        59691
#dichotomies:   44219
#leaf labels:   59691
#inner labels:  41753
Number of new sequences added this iteration
149 alignment_names_new.txt

• I have further automated the process so that the excluded_sequences.tsv file auto-updates. This removes the last human interaction that is required to run the iterative script. The key difference now is that the this file and the ft_SH.tree file are copied from the previous iteration (specified via -p) at the start of the analysis.

• None