ammaraziz/flukit

Flukit - simple variant caller for influenza

Used interally at WHOFLUCC. Not recommended for external usage.

install

1. clone this repo
2. install using pip

cd flukit && python -m pip install .

3. Install nextclade:

conda install -c bioconda nextclade

usage

Run flukit --help to see detailed instructions

• input
  • fasta, file with headers ending in .1... .4 which represent the gene. For example: MySample.4 is the HA gene of MySample.
  • lineage, one of h1n1, h3n2, vic
  • the batch name used as prefix for output files
  • the output path

Example:

flukit -s flu.fasta -l h3n2 -b batch150 -o ~/Desktop/

• output
  • tsv file in the following format:

   seqno - the fasta header
   ha_aa - HA mutations called against vacc_ref
   na - H275Y mutation
   mp - S31N mutation
   pa - I38X mutation
   vacc_ref - called against ancestral strains
  

Output is formatted specifically for internal database.