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Software Open Access

roblanf/sarscov2phylo: 28-10-20

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
122740
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 120561
Alignment length:    29903
Total # residues:    3592959392
Smallest:            25059
Largest:             29903
Average length:      29802.0
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 120561
Alignment length:    29903
Total # residues:    3576678015
Smallest:            24962
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: 120367
Alignment length:    29903
Total # residues:    3570946321
Smallest:            28961
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: 120367
Alignment length:    29646
Total # residues:    3561657772
Smallest:            28437
Largest:             29646
Average length:      29590.0
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 209776
#leaves:    120275
#dichotomies:   84953
#leaf labels:   120275
#inner labels:  79848
Number of new sequences added this iteration
5293 alignment_names_new.txt
Notable changes to the scripts in this release
  • None
Notable aspects of the trees
  • None

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