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usage.md

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Usage

Simple usage

By default hedgehog will run the custom lineage set model to assign the most likely lineage set out of currently designated lineages that have been included in the custom spike assignment pangoLEARN model.

  1. Activate the environment conda activate hedgehog
  2. Run hedgehog <query>, where <query> is the name of your input file

To find out which lineage release is included in the lineage sets type:

hedgehog -pv
or 
hedgehog --pango-version

Full usage

usage: hedgehog <query> [options]
  
hedgehog: SARS-CoV-2 Spike-sequence based lineage set assignment

positional arguments:
  query                 Query (multi-)fasta file of spike 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_set_report.csv
  --tempdir TEMPDIR     Specify where you want the temp stuff to go. Default: $TMPDIR
  --no-temp             Output all intermediate files, for dev purposes.
  --max-ambig MAXAMBIG  Maximum proportion of Ns allowed for hedgehog to attempt assignment. Default: 0.1
  --min-length MINLEN   Minimum query length allowed for hedgehog to attempt assignment. Default: 3800
  --verbose             Print lots of stuff to screen
  -t THREADS, --threads THREADS
                        Number of threads
  -v, --version         show program's version number and exit
  -pv, --pango-version  show pango designation version number and exit

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