Main tool : pangolin
Full documentation: https://cov-lineages.org/resources/pangolin.html
Phylogenetic Assignment of Named Global Outbreak LINeages
Additional tools:
- pangolin-data 1.23.1
- pangolin-assignment 1.23.1
- minimap2 2.26-r1175
- usher 0.6.2
- faToVcf 448
- scorpio 0.3.19
- constellations 0.1.12
- gofasta 1.2.1
- mafft 7.520
- python 3.8.18
This docker image contains usher version 0.6.2. This version of usher has a bug that can cause some lineage A samples to be assigned to A.* sublineages or even B or B.* sublineages.
If you are running pangolin on early 2020 sequences that may be lineage A, it is highly recommended to use the assignment cache (and upgrade to usher 0.6.3 when it is available) See the pangolin-assignment v1.23 release page for more details
We plan to upgrade usher to >=0.6.3 in the next release of this docker image.
As of pangolin version 4.3, pangoLEARN mode has been deprecated. More info can be found here on the v4.3 release page.
If
--analysis-mode fastor--analysis-mode pangolearnis given, pangolin v4.3 will print out a warning and use UShER mode instead, unless--datadiris also given specifying a directory with pangoLEARN model files. The next release of pangolin-data (v1.20) will no longer include the model files which have not been updated since v1.18.
This docker image contains pangolin-data v1.23.1. The pangoLEARN model has not been updated since pangolin-data version 1.18. Only the the underlying UShER tree/protobuf file will be maintained for the forseeable future.
Please use the UShER mode of pangolin if you want to stay up-to-date with the most recent lineages. See pangolin-data release notes here for more details
# run Pangolin in the default mode (usher). Can optionally supply --analysis-mode usher
$ pangolin /pangolin/pangolin/test/test_seqs.fasta -o /data/test_seqs-output-pusher
# view the output CSV
$ column -t -s, /data/test_seqs-output-pusher/lineage_report.csv
taxon lineage conflict ambiguity_score scorpio_call scorpio_support scorpio_conflict scorpio_notes version pangolin_version scorpio_version constellation_version is_designated qc_status qc_notes note
India seq B.1.617.1 0.0 B.1.617.1-like 1.0 0.0 scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Oth alleles 0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: B.1.617.1(1/1)
b117 B.1.1.7 0.0 Alpha (B.1.1.7-like) 0.91 0.04 scorpio call: Alt alleles 21; Ref alleles 1; Amb alleles 1; Oth alleles 0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: B.1.1.7(2/2)
outgroup_A A 0.0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: A(1/1)
issue_57_torsten_seq Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
This_seq_has_6000_Ns_in_18000_bases Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
This_seq_has_no_seq Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
This_seq_is_too_short Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail Ambiguous_content:0.9
This_seq_has_lots_of_Ns Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail Ambiguous_content:0.98
This_seq_is_literally_just_N Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
Japan_seq B 0.0 PANGO-v1.16 4.1.3 0.3.17 v0.1.10 True pass Ambiguous_content:0.02 Assigned from designation hash.
USA_seq B.1.314 0.0 PANGO-v1.16 4.1.3 0.3.17 v0.1.10 True pass Ambiguous_content:0.02 Assigned from designation hash.
Unassigned_omicron_seq BA.1 0.0 Probable Omicron (BA.1-like) 0.71 0.08 scorpio call: Alt alleles 42; Ref alleles 5; Amb alleles 9; Oth alleles 3 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.03 Usher placements: BA.1(1/1)