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  1. Technical Descriptions

SARS-CoV-2 Genome Tree

How SARS-CoV-2 trees are constructed in Pathogenwatch.

PreviousSARS-CoV-2 Notable MutationsNextCore Genome Tree

Last updated 11 months ago

About

Pathogenwatch will automatically generate a tree of SARS-CoV-2 genomes when a collection is created from the . When each genome is uploaded to Pathogenwatch an alignment against the Wuhan Hu 1 reference genome is stored. The selected genomes are aligned into a multiple sequence alignment and a dendrogram produced using . This tree is then displayed in the interactive collection viewer.

Method

Alignment

  • The aligned FASTA output is stored in Pathogenwatch.

Tree Building

  • The FASTA files are concatenated into a multiple sequence alignment along with the wuhan-hu-1 reference.

  • Root the resulting tree to the reference.

  • Remove the reference from the tree.

References

Each genome is mapped against the wuhan-hu-1 reference genome () using .

The resulting SAM file from each genome is converted into FASTA format using .

Run with the options -gtr -nosupport -nt.

FastTree: Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490. .

goFASTA:

minimap2: Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100.

📖
NCBI Reference Sequence: NC_045512.2
minimap2
goFASTA
FastTree
doi:10.1371/journal.pone.0009490
https://github.com/cov-ert/gofasta
doi:10.1093/bioinformatics/bty191
Genome Browser
FastTree
SARS-CoV-2 tree built using the Pathogenwatch pipeline.