pangolin v1.0.2

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.

pangolin v1.0

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.