UPDATE: Legacy config.yaml file bug fix.
Phylogenetic Assignment of Named Global Outbreak LINeages
pangolin is a tool that assigns global lineages from hCoV-2019/lineages to a query fasta file.
In this release, pangolin relies on being run within the pangolin conda environment. The environment file that comes with the repository will install all dependencies and data required to run pangolin.
Current usage:
pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages
positional arguments:
query
optional arguments:
-h, --help show this help message and exit
-o OUTDIR, --outdir OUTDIR
Output directory
-d DATA, --data DATA Data directory minimally containing a fasta alignment
and guide tree
-n, --dry-run Go through the motions but don't actually run
-f, --force Overwrite all output
--tempdir TEMPDIR Specify where you want the temp stuff to go. Default:
$TMPDIR
--max-ambig MAXAMBIG Maximum proportion of Ns allowed for pangolin to
attempt assignment. Default: 0.5
--min-length MINLEN Minimum query length allowed for pangolin to attempt
assignment. Default: 10000
-t THREADS, --threads THREADS
Number of threads
-v, --version show program's version number and exit
-lv, --lineages-version
show lineages's version number and exit
Current output includes lineage designation, aLRT, UFbootstrap from iqtree, version of the data used, whether the query sequence passed qc and a note to explain why it failed if it didn't.