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@roblanf roblanf released this 14 Jun 04:08
· 189 commits to master since this release
12-6-20
4953975

The trees in this release were generated with the following command line:

bash global_tree_gisaid.sh -i gisaid_hcov-19_2020_06_11_21.fasta -o global.fa -t 33

The raw sequence file contains all available SARS-CoV-2 genomes in GISAID available on the 12th of June 2020, at 9PM Canberra (Australia) time.

The ZIP file contains the code necessary to reproduce the trees themselves, and the README in the zip file also describes the methods used in detail. I also include the trees themselves here so that they can be easily downloaded without downloaded the entire repo.

Filtering statistics

Note: these are now provided in the alignments.log file if you run the script.

alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 45495
Alignment length:    29903
Total # residues:    1344997236
Smallest:            64
Largest:             29903
Average length:      29563.6
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 45495
Alignment length:    29903
Total # residues:    1338465117
Smallest:            64
Largest:             29718
Average length:      29420.0
Average identity:    100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 39929
Alignment length:    29903
Total # residues:    1179699101
Smallest:            27973
Largest:             29718
Average length:      29544.9
Average identity:    100%
//
alignment stats of global alignment after trimming sites that are >50% gaps
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 39929
Alignment length:    29718
Total # residues:    1179699101
Smallest:            27973
Largest:             29718
Average length:      29544.9
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:	Phylogram
#nodes:	72867
#leaves:	39850
#dichotomies:	31971
#leaf labels:	39850
#inner labels:	33015

Notable changes to the scripts in this release

  • Alignments are now done by profile aligning direct to WH1, to preserve information on base positions
  • Trees now include polytomies
  • gotree is now used to calculate TBE and FBP values, because it can handle polytomies
  • Only sites that are >50% gaps are removed. This is done after changing N's to gaps in the alignment (see readme for details). In practice so far this means that only those sites which are first masked are then removed
  • The scripts were fairly extensively changed, so it is worth going through the readme because the methods are now quite different

Notable aspects of the trees

  • There are a couple of samples on long branches there were not removed by treeshrink. Some caution is warranted with these samples.
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