Main tool : piranha
Full documentation: https://github.com/polio-nanopore/piranha
Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis.
piranha is a tool in development as part of the Poliovirus Sequencing Consortium. It runs an automated analysis pipeline for sequencing VP1 regions of the poliovirus or non-polio enterovirus genome (whole genome analysis to be implemented soon) and produces an interactive report alongside the consensus data.
Additional tools:
- samtools/bcftools/tabix 1.11
- minimap2 2.17
- gofasta 1.1.0
- mafft 7.508
- racon 1.5.0
- medaka 1.7.2
- python 3.9.9
- biopython 1.79
- snakemake-minimal 7.17.1
# run Piranha on a directory of FASTQs (Guppy output)
piranha -i /piranha/test/pak_run/demultiplexed --verbose -b piranha/test/pak_run/barcodes01.csv -t 2 2>&1 | tee piranha.log