roblanf/sarscov2phylo: 22-7-20

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

bash global_tree_gisaid.sh -i gisaid_hcov-19_2020_07_22_07.fasta -o global.fa -t 34

The raw sequence file contains all available SARS-CoV-2 genomes in GISAID available on the 22nd of July 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 downloading the entire repo.

Filtering statistics

sequences downloaded from GISAID
44915
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 44446
Alignment length:    29903
Total # residues:    1326206221
Smallest:            29146
Largest:             29903
Average length:      29838.6
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 44446
Alignment length:    29903
Total # residues:    1318812088
Smallest:            29059
Largest:             29680
Average length:      29672.2
Average identity:    100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 44278
Alignment length:    29903
Total # residues:    1313831108
Smallest:            29059
Largest:             29680
Average length:      29672.3
Average identity:    100%
//
alignment stats of global alignment after trimming sites that are >50% gaps
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 44278
Alignment length:    29661
Total # residues:    1310443036
Smallest:            28457
Largest:             29661
Average length:      29595.8
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:   Phylogram
#nodes: 79266
#leaves:        44233
#dichotomies:   33504
#leaf labels:   44233
#inner labels:  35031

Notable changes to the scripts in this release

• None

Notable aspects of the trees

• A few long branches, particularly on sequences from India. These could be real or due to a lot of sequencing error. If real they would suggest that there are some highly diverged sequences in India. They should be treated with additional diligence compared to other sequences.