Authors: V. Murigneux, L. W. Roberts, B. M. Forde, M. D. Phan, N. T. K. Nhu, A. D. Irwin, P. N. A. Harris, D. L. Paterson, M. A. Schembri, D. M. Whiley, S. A. Beatson
Date Published: 25th Jun 2021
Publication Type: Journal
PubMed ID: 34172000
Citation: BMC Genomics. 2021 Jun 25;22(1):474. doi: 10.1186/s12864-021-07767-z.
microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.
To build microPIPE we evaluated the performance of several tools at each step of bacterial genome assembly, including basecalling, assembly, and polishing. Results at each step were validated using the high-quality ST131 Escherichia coli strain EC958 (GenBank: HG941718.1). After appraisal of each step, we selected the best combination of ...
COVID-19: variation analysis on ARTIC ONT data
This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...
Creator: Wolfgang Maier
Submitter: WorkflowHub Bot
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 ‘N’.
Creator: David F. Nieuwenhuijse, Alexey Sokolov
Submitter: Ross Thorne