4 items tagged with 'ONT'.
Work-in-progress
A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using āNā.
Created: 12th Feb 2021 at 11:46
Created: 5th Aug 2020 at 14:05
Genome assembly: Unicycler-based WF for Klebsiella pneumoniae [Wick et al. Microbial genomics 2017]
Created: 5th Aug 2020 at 14:03
Genome assembly: Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018]
Created: 5th Aug 2020 at 14:01