ARTIC Fieldbioinformatics is a pipeline and set of accompanying tools for working with viral nanopore sequencing data, generated from tiling amplicon schemes.

Fieldbioinformatics is a python based pipeline which takes read FASTQs generated by during viral amplicon sequencing and assembles them into a FASTA consensus sequence.

Features include:

  • read filtering
  • primer trimming
  • amplicon coverage normalisation
  • variant calling
  • consensus building

History

The analytical approach Fieldbioinformatics utilises was first developed to analyse Ebola virus sequencing data during the 2014-16 West African Ebola outbreak, it was then developed into a dedicated automatic pipeline as part of the ZIBRA project to do genomic surveillance of the Zika virus outbreak.

Usage

Fieldbioinformatics is a single-sample, Nanopore specific, pipeline meaning that it can only be used to run a single sample at a time and only using data generated by nanopore sequencing. If you are interested in running multiple samples simultaneously or have Illumina data, then we recommend amplicon-nf which is a Nextflow pipeline far better suited to this usecase.