Title: roblanf/sarscov2phylo: 22-09-20
Type Software roblanf, Richard Mansfield (2020): roblanf/sarscov2phylo: 22-09-20. Zenodo. Software. https://zenodo.org/record/4057189
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 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 75617 // alignment stats of global alignment Alignment number: 1 Format: aligned FASTA Number of sequences: 73023 Alignment length: 29903 Total # residues: 2176708899 Smallest: 29018 Largest: 29903 Average length: 29808.5 Average identity: 100% // alignment stats of global alignment after masking sites Alignment number: 1 Format: aligned FASTA Number of sequences: 73023 Alignment length: 29903 Total # residues: 2166330884 Smallest: 28922 Largest: 29675 Average length: 29666.4 Average identity: 100% // alignment stats after filtering out short/ambiguous sequences Alignment number: 1 Format: aligned FASTA Number of sequences: 72833 Alignment length: 29903 Total # residues: 2160703716 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: 72833 Alignment length: 29660 Total # residues: 2155121794 Smallest: 28437 Largest: 29660 Average length: 29589.9 Average identity: 100% // After filtering sequences with TreeShrink Type: Phylogram #nodes: 129415 #leaves: 72786 #dichotomies: 54008 #leaf labels: 72786 #inner labels: 50974 Number of new sequences added this iteration 1437 alignment_names_new.txt Notable changes to the scripts in this release I have switched to using a GISAID datastream to download the sequence data, using the following command, which essentially replicates what I was doing before: 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_virus_name + "|" + .covv_accession_id + "|" + .covv_collection_date + "\n" + .sequence] | join("\n")' \ | xz -c -T22 > gisaid-${DATE}.fasta.xzwhere $DATE is the date in the title of this release, but in the format YYYY-MM-DD, e.g. 2020-09-22
Notable aspects of the trees NoneMore information
- DOI: 10.5281/zenodo.4057189
Dates
- Publication date: 2020
- Issued: September 29, 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/22-09-20 | ||
IsVersionOf | https://doi.org/10.5281/zenodo.3958883 | ||
IsPartOf | https://zenodo.org/communities/covid-19 | ||
IsPartOf | https://zenodo.org/communities/zenodo |