An initial repository for keeping and sharing simple scripts and tools mainly used to manipulate and organise pathogen WGS pipeline output data.
This script will go through the output of a nf-flu run and collate some coverage stats into a csv table.
Usage example: python nf-flu_cov_stats_collator.py -i path/to/nf-flu/output
To see other options: python nf-flu_cov_stats_collator.py -h
This script will go through the output of a nf-flu run and collate segment fasta files into one or more multifastas. These can then be used as input for nextclade.
Usage example: python nf-flu_segment_fasta_collator.py -i path/to/nf-flu/output
To see other options: python nf-flu_segment_fasta_collator.py -h