Skip to content

14-6-20
Compare
Choose a tag to compare
@roblanf roblanf released this 16 Jun 01:22
· 185 commits to master since this release
14-6-20
b64af4b

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

bash global_tree_gisaid.sh -i gisaid_hcov-19_2020_06_14_04.fasta -o global.fa -t 30

The raw sequence file contains all available SARS-CoV-2 genomes in GISAID available on the 14th 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.

sequences downloaded from GISAID
46304
//
alignment stats of global alignment
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 46249
Alignment length:    29903
Total # residues:    1367525290
Smallest:            64
Largest:             29903
Average length:      29568.8
Average identity:    100%
//
alignment stats of global alignment after masking sites
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 46249
Alignment length:    29903
Total # residues:    1360867101
Smallest:            64
Largest:             29718
Average length:      29424.8
Average identity:    100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 40627
Alignment length:    29903
Total # residues:    1207019620
Smallest:            28249
Largest:             29718
Average length:      29709.8
Average identity:    100%
//
alignment stats of global alignment after trimming sites that are >50% gaps
Alignment number:    1
Format:              aligned FASTA
Number of sequences: 40627
Alignment length:    29718
Total # residues:    1200334988
Smallest:            27973
Largest:             29718
Average length:      29545.3
Average identity:    100%
//
After filtering sequences with TreeShrink
Type:	Phylogram
#nodes:	74240
#leaves:	40585
#dichotomies:	32600
#leaf labels:	40585
#inner labels:	33653

Notable changes to the scripts in this release

  • All sequences identified by treeshrink are now removed from the excluded_sequences.tsv, since treeshrink seemed to be iteratively removing more and more sequences.

Notable aspects of the trees

  • There are some long branches in the trees, and one clade in particular that appears to have a lot of mutations. I am unsure whether this clade (and the branchlenghts leading to it) are legitimate. However, I have checked out a handful of the seuqences in this clade in the alignment (e.g. hCoV-19/Australia/VIC35/2020|EPI_ISL_419755|2020-03-10) and there is nothing obviously odd in the alignment itself. Some caution is warranted around this clade though.
Assets 4
Loading