pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages
positional arguments:
query Query fasta file of sequences to analyse.
optional arguments:
-h, --help show this help message and exit
-o OUTDIR, --outdir OUTDIR
Output directory. Default: current working directory
--outfile OUTFILE Optional output file name. Default: lineage_report.csv
-d DATADIR, --datadir DATADIR
Data directory minimally containing a fasta alignment
and guide tree
--tempdir TEMPDIR Specify where you want the temp stuff to go. Default:
$TMPDIR
--no-temp Output all intermediate files, for dev purposes.
--decompress-model Permanently decompress the model file to save time
running pangolin.
--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
--panGUIlin Run web-app version of pangolin
--verbose Print lots of stuff to screen
-v, --version show program's version number and exit
-pv, --pangoLEARN-version
show pangoLEARN's version number and exit
--update Automatically updates to latest release of pangolin
and pangoLEARN, then exits