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Marit Hetland edited this page Feb 17, 2021 · 6 revisions

susCovONT

Pipeline to generate consensus.fasta files and identify pangolin lineage and nextstrain clade of Sars-CoV-2 genomes from ONT sequencing.

This pipeline runs artic guppyplex, artic minion (with nanopolish), pangolin and nextclade. Whilst these tools are easy to use and run by themselves, this pipeline puts them together and creates an output run report combining the results from all three programs. It also prepares the run folder structure for storing. This is so all ONT sequencing runs of Sars-CoV-2 will have the same folder structure and same format of the output reports - for each concatenation or collection of data.

This pipeline takes as input a folder with name <run_name> which contains the folders fast5_pass and fastq_pass from Sars-CoV-2 ONT sequencing together with a CSV-file which links barcode and sample name, and it outputs consensus.fasta files along with <run_name>_report.csv which includes pangolin lineage, nextstrain clade, mutations and QC.

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