MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

Abstract

Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers; however, easy and automated construction of high-quality bacterial genomes remains challenging. Here we present MicroPIPE: a reproducible end-to-end bacterial genome assembly pipeline for ONT and Illumina sequencing. To construct MicroPIPE, we evaluated the performance of several tools for genome reconstruction and assessed overall genome accuracy using ONT both natively and with Illumina. Further validation of MicroPIPE was carried out using 11 sequence type (ST)131 Escherichia coli and eight publicly available Gram-negative and Gram-positive bacterial isolates. MicroPIPE uses Singularity containers and the workflow manager Nextflow and is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe.

Clinical Burkholderia pseudomallei isolates from Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains

“…Illumina reads were trimmed with Trimmomatic v0.36[8] and quality assessed with multiQC[9], genomes were assembled with SPAdes v3.14.0[10] and annotated with Prokka v1.13[11]. Long reads were filtered, quality checked, assembled, and polished with Illumina reads where applicable using the MicroPIPE pipeline[12]. Genomes derived from this study are publicly available at NCBI BioProject ID: PRJNA717363.…”

Portable nanopore-sequencing technology: Trends in development and applications

“…In contrast to previous work, in Faure et al (2021) , the authors present GraphUnzip, a fast, memory-efficient, and accurate tool that generates high-quality gap-less supercontigs by connecting only sequences that overlap potential links. In Murigneux et al (2021) , the authors present an easy-access, integrated solution for attaining high-quality bacterial genomes by combining ONT with Illumina sequencing to create MicroPIPE, an end-to-end process for assembling bacterial genomes. However, the development of relevant bioinformatic tools, mainly quantitative analysis tools, is still insufficient.…”