preprocessing and assembly workflows for nanopore data
The NanoporeGuppyAssembly.wdl workflow was developed for the preprocessing and assembly of Oxford Nanopore sequencing of SARS-CoV-2 ro be run on the GCP Terra platform. It takes basecalled fastq files as input (e.g. from MinKNOW).
The columns for the input data table in Terra should be arranged as:
- entity:sample_id (column of sample names/ids). If there is more than on
This is a companion discussion topic for the original entry at github.com/CDPHE/nanopore-preprocessing-assembly