pangolin v4.0.3

Release notes

Updates include

• Run git-lfs install before pangolin-assignment installation (resolves issue #403)
• Ignore cache row is lineage is unassigned (resolves issue #410).
• Failed to map sequences found again, resolves issue #409
• Updating CLI help message for analysis mode to make clearer as suggested by #396
• As suggested in #412, scorpio-only mode introduced (docs updated at https://cov-lineages.org/resources/pangolin/usage.html). version field in the output file in this mode now indicates scorpio mode was used and the number corresponds to the version of constellations used in the assignment, e.g. SCORPIO_v0.1.4 instead of PUSHER_v1.2.333 or PLEARN_v1.2.333
• Adding in cleanup step for issue #401
• Adding in --max-ambig and --min-length logic flagged in issue #405

pangolin v4.0.2

Release notes

• Introducing ram warning for pangoLEARN mode
• PR 404 merged in avoiding piping in UShER mode
• pysam dependency removed

pangolin v4.0.1

Release notes

• RAM warning in pangoLEARN mode (issue #395)
• --all-versions doesn't include mode type print out now, print out happens later
• Parentheses in file name no longer break (issue #397)

pangolin v4.0

Release notes

pangolin has had a big code overhaul recently, which should help with maintainability going forward, but there are some main changes the user will be concerned with that I wanted to flag here before the release:

• Notably, the default mode is shifting from pangoLEARN to UShER. If you run large amounts of sequences through pangolin routinely you should be aware this update will impact the speed of pangolin for large amounts of data and you may want to consider parallelisation, using the optional usher assignment cache file (accessed with --add-assignment-cache and --use-assignment-cache flags) or using the --analysis-mode pangoLEARN flag.
• The pangoLEARN model being trained is a random forest rather than a decision tree, so the confidence scores reflect the assignment probability from the random forest model now rather than the number of suitable categories as is the case with the decision tree model.
• Changes to dependencies: We’re rationalising the pangoLEARN repository and the file accessed from pango-designation into a single repository called pangolin-data, so pangoLEARN and pango-designation are no longer needed as dependencies.
• Changes to versioning: pangolin-data will have the same version number as the pango-designation tag as the lineages version in UShER protobuf file and the pangoLEARN model, giving a less convoluted versioning system than has previously been the case.
• There’s been confusion around the word None when a sequence fails to be assigned a lineage so we’ve changed the reporting from None to Unassigned as we think this is clearer.
• The output csv file has changed slightly. We’ve tried to keep it as consistent as possible, but the versioning has changed so the columns reflect that. We’ve added in the pangolin version and we’ve separated out qc notes into a separate column to other notes to make it easier to access specific bits of information. New output format found here: https://cov-lineages.org/resources/pangolin/output.html
• Because the location of the data files will now fall in a different repository (pangolin_data), there isn’t any natural backwards compatibility. We’re intending on training the decision tree model as well for the next couple of releases to give a buffer period where the data for 3.0 and 4.0 are both available with their respective inputs, and have been training the decision tree model for a tandem pangoLEARN and pangolin-data release this week. This will likely get phased out eventually as everyone migrates to v4.0.
• Expanded lineage flag feature from issue #261 by @baileyglen
• Optional use of assignment-cache for usher speed up with pangolin --use-assignment-cache.
• The mapping command minimap2 uses has been altered slightly with --score-N=0 and mode -x asm20 being run now.
• Alignment, sequence QC, Scorpio classification and designation hash assignment are run on all sequences now (previously only sequences that passed QC had these steps run). Bear in mind low quality sequences may fail to map, and sequences that fail QC will still not recieve a final lineage call, but information about what calls scorpio provides may be available.
• When updating, please bear in mind installation via this repo will always provide the latest version (check the tagged releases). Installation through bioconda may have a lag for latest version to be available for install. Similarly, the pangolin web application is maintained by the Centre for Genomic Pathogen Surveillance (for which we are very grateful!) and users should be aware there may also be a short lag for update.

How to report issues

Please report any software issues that might arise to this repository and we will address them as soon as possible. Any lineage misassignments or new lineage requests please report to pango-designation.

pangolin v3.1.20

Update to fix false positive Omicron BA.1.1 calls

pangolin v3.1.19

Small fix

pangolin v3.1.18

Minor release to improve confusion over B.1.1.529 calls:
The lineage call B.1.1.529 is misleading as there are no designated sequences for this label and it usually instead indicates lower quality/contaminated sequences that could not be well assigned. We want to remove it as a possibility. This change handles the case where the constellation file has mrca_lineage:"None" and allows this to override a lineage call.

pangolin v3.1.17

• Update minimap2 flags to improve alignment with more diverged sequences and avoid patches of Ns
• Bugfix to remove missed false positive VOC/VUI calls
• Pangolin update should check if pre-release

pangolin v3.1.16

Release notes

• Remove duplicated print when scorpio makes assignment None (#340)
• PR merged from @matt-sd-watson to enable pangolin to read from stdin (#334)
• Bug fix for how pangolin handles QC, no longer holds records in memory (#330)
• Fixing pandas incompatibility for issue #332

pangolin v3.1.15

Release notes

• Merging PR #319 and #320
• Addressing issue #277 for usher dependency, now only check usher in environment if usher flag used
• Merging PR #325 and #324
• Stripping out leading v and adding update code to utils file rather than master command.py file
• Addressing issue #321, bioconda made less specific
• Added UShER mode test to github actions