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.
Fieldbioinformatics SOP
Fieldbioinformatics: viral amplicon sequencing bioinformatics SOP
Nanopore | bioinformatics