MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.

Abstract (Expand)

BACKGROUND: Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and … automated construction of high-quality bacterial genomes using nanopore reads remains challenging. Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing. RESULTS: We evaluated the performance of several popular tools used during genome reconstruction, including base-calling, filtering, assembly, and polishing. We also assessed overall genome accuracy using ONT both natively and with Illumina. All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. Software chosen at each stage were incorporated into our final pipeline, MicroPIPE. Further validation of MicroPIPE was carried out using 11 additional ST131 E. coli isolates, which demonstrated that complete circularised chromosomes and plasmids could be achieved without manual intervention. Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. We found that revised basecalling and updated assembly of the majority of these genomes resulted in improved accuracy compared to the current publicly available complete genomes. CONCLUSIONS: MicroPIPE is built in modules using Singularity container images and the bioinformatics workflow manager Nextflow, allowing changes and adjustments to be made in response to future tool development. Overall, MicroPIPE provides an easy-access, end-to-end solution for attaining high-quality bacterial genomes. MicroPIPE is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe .

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

ERGA Assembly Galaxy HiFi & HiC Pipelines

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads

Executing all workflows will output two, scaffolded, haplotype assemblies

Maintainers: Tom Brown, Diego De Panis

Number of items: 6

Tags: Assembly, Bioinformatics, Galaxy, Genomics, ONT, Genome assembly, HiFi

ERGA DataQC ONT v2305 (WF0)

Oxford Nanopore QC pipeline which calculates basic statistics as well as filtering for longest reads and creating QC plots using Nanoplots

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Tom Brown

Master of Pores 2

MoP2- DSL2 version of Master of Pores

Docker Build Status mop2-CI License: MIT [![Nextflow ...

Type: Nextflow

Creators: None

Submitter: Luca Cozzuto

microPIPE: a pipeline for high-quality bacterial genome construction using ONT and Illumina sequencing
Stable

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 ...

Type: Nextflow

Creators: Valentine Murigneux, Leah W Roberts,  Brian M Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam D Irwin, Patrick N A Harris, David L Paterson, Mark A Schembri, David M Whiley, Scott A Beatson 

Submitter: Valentine Murigneux

DOI: 10.48546/workflowhub.workflow.140.1

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sars-cov-2-ont-artic-variant-calling/COVID-19-ARTIC-ONT

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 ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

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ENA SARS-CoV-2 Nanopore Amplicon Sequencing Analysis Workflow
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 ‘N’.

Type: Nextflow

Creator: David F. Nieuwenhuijse, Alexey Sokolov

Submitter: Ross Thorne

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ONT -- Metagenomics-Kraken2-Krona

Metagenomics: taxa classification

Type: Galaxy

Creator: Milad Miladi

Submitter: Willem de Koning

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ONT - Workflow-Wick-et.al.

Genome assembly: Unicycler-based WF for Klebsiella pneumoniae [Wick et al. Microbial genomics 2017]

Type: Galaxy

Creator: Milad Miladi

Submitter: Willem de Koning

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ONT -- Assembly-Flye-AhrensLab

Genome assembly: Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018]

Type: Galaxy

Creator: Milad Miladi

Submitter: Willem de Koning

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