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pangolin docker image

Main tool : pangolin

Full documentation: https://cov-lineages.org/resources/pangolin.html

Phylogenetic Assignment of Named Global Outbreak LINeages

Additional tools:

Rare bug warning ⚠️

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.

pangoLEARN deprecation

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 fast or --analysis-mode pangolearn is given, pangolin v4.3 will print out a warning and use UShER mode instead, unless --datadir is 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

Example Usage

# 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)