Main tool : pangolin
Full documentation: https://cov-lineages.org/resources/pangolin.html
Phylogenetic Assignment of Named Global Outbreak LINeages
Additional tools:
- pangolin-data 1.24
- pangolin-assignment 1.24
- minimap2 2.26-r1175
- usher 0.6.3
- faToVcf 448
- scorpio 0.3.19
- constellations 0.1.12
- gofasta 1.2.1
- mafft 7.520
- python 3.8.18
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 v1.24. 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)