A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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GFF included repo doesn't include ORF1ab frameshift #110
Is the GFF included in the repo intended for production use or is it only for unit testing?
https://github.com/connor-lab/ncov2019-artic-nf/blob/9ac3119a875d75c49de65848a3587e6fcec22d1c/typing/MN908947.3.gff
The GFF included in the repo seems to use coordinates for the ORF1ab gene that do not take into account 1bp frameshift due to ribosomal slippage:
This frameshift is seen in the latest NCBI GFF: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz