Title: roblanf/sarscov2phylo: 18-10-20
Type Software roblanf, Richard Mansfield (2020): roblanf/sarscov2phylo: 18-10-20. Zenodo. Software. https://zenodo.org/record/4145970
Links
- Item record in Zenodo
- Digital object URL
Summary
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
If you publish papers that use this tree you must still follow the GISAID data sharing and attribution rules.
DetailsThe 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 108202 // alignment stats of global alignment Alignment number: 1 Format: aligned FASTA Number of sequences: 106464 Alignment length: 29903 Total # residues: 3173059520 Smallest: 29030 Largest: 29903 Average length: 29804.1 Average identity: 100% // alignment stats of global alignment after masking sites Alignment number: 1 Format: aligned FASTA Number of sequences: 106464 Alignment length: 29903 Total # residues: 3158473719 Smallest: 28961 Largest: 29675 Average length: 29667.1 Average identity: 100% // alignment stats after filtering out short/ambiguous sequences Alignment number: 1 Format: aligned FASTA Number of sequences: 106273 Alignment length: 29903 Total # residues: 3152816993 Smallest: 28961 Largest: 29675 Average length: 29667.1 Average identity: 100% // alignment stats of global alignment after trimming sites that are >50% gaps Alignment number: 1 Format: aligned FASTA Number of sequences: 106273 Alignment length: 29646 Total # residues: 3144363035 Smallest: 28437 Largest: 29646 Average length: 29587.6 Average identity: 100% // After filtering sequences with TreeShrink Type: Phylogram #nodes: 186198 #leaves: 106272 #dichotomies: 75928 #leaf labels: 106272 #inner labels: 71407 Number of new sequences added this iteration 340 alignment_names_new.txt Notable changes to the scripts in this release Some more issues occurred with sequence names, so I have shifted to using exclusively just the EPI-IDs for sequence names in the alignments, trees, and scripts. This should avoid any future issues with sequence names.If you have a GISAID data stream, this means you can get the data as follows:
curl -u "${GISAID_LOGIN}:${GISAID_PASSWORD}" ${URL} 2>/dev/null \ | xz -d -T22 \ | jq -r 'select(.covv_subm_date <= "'"$DATE"'" and .is_complete == true and .is_high_coverage == true) | [">" + .covv_accession_id + "\n" + .sequence] | join("\n")' \ | xz -c -T22 > gisaid-${DATE}.fasta.xz Notable aspects of the trees Names have changed to include only the EPI-IDs. This has the side-benefit of roughly halving the size of the tree file.More information
- DOI: 10.5281/zenodo.4145970
Dates
- Publication date: 2020
- Issued: October 28, 2020
Rights
- info:eu-repo/semantics/openAccess Open Access
Format
electronic resource
Relateditems
| Description | Item type | Relationship | Uri |
|---|---|---|---|
| IsSupplementTo | https://github.com/roblanf/sarscov2phylo/tree/18-10-20 | ||
| IsVersionOf | https://doi.org/10.5281/zenodo.3958883 | ||
| IsPartOf | https://zenodo.org/communities/covid-19 | ||
| IsPartOf | https://zenodo.org/communities/zenodo |