nf-core/taxprofiler and nf-core/createtaxdb provide scalable and reproducible metagenomic multi-classifier database construction and taxonomic profiling
Metagenomic taxonomic classification addresses the problem of efficiently characterising the taxonomic sources of all DNA sequences extracted from a sample. A common approach to address the differences and biases among the many different available taxonomic classification tools is to analyse metagenomic data using multiple classifiers and databases. However, manual both classifier database construction and the classification itself can beare time- and computational resource-intensive tasks due to the heterogeneous inputs and configuration of the toolswhen performed manually, particularly when combined with the appropriate preprocessing of sequencing reads before classification. Here we present two companion Nextflow best-practice pipelines, nf-core/taxprofiler and nf-core/createtaxdb, that parallelise taxonomic classification database construction and taxonomic profiling with multiple classifiers. Designed for versatile metagenomic profiling of short and long reads, the pipelines offer automated pre-processing and classification of metagenomic data with up to 14 classifiers, as well as common post-processing steps and standardised output files. In this article, we describe the implementation of the two pipelines, provide generalised guidance on the computational resource requirements of each pipeline on typical metagenomic datasets, and illustrate the application of the two pipelines within a theoretical clinical metagenomics analysis context. Together, the two pipelines offer researchers flexible, scalable, and portable pipelines for reproducible metagenomic classifications applicable to any area of microbiology.
Metagenomic taxonomic classification addresses the problem of efficiently characterising the taxonomic sources of all DNA sequences extracted from a sample. A common approach to address the differences and biases among the many different available taxonomic classification tools is to analyse metagenomic data using multiple classifiers and databases. However, manual both classifier database construction and the classification itself can beare time- and computational resource-intensive tasks due to the heterogeneous inputs and configuration of the toolswhen performed manually, particularly when combined with the appropriate preprocessing of sequencing reads before classification. Here we present two companion Nextflow best-practice pipelines, nf-core/taxprofiler and nf-core/createtaxdb, that parallelise taxonomic classification database construction and taxonomic profiling with multiple classifiers. Designed for versatile metagenomic profiling of short and long reads, the pipelines offer automated pre-processing and classification of metagenomic data with up to 14 classifiers, as well as common post-processing steps and standardised output files. In this article, we describe the implementation of the two pipelines, provide generalised guidance on the computational resource requirements of each pipeline on typical metagenomic datasets, and illustrate the application of the two pipelines within a theoretical clinical metagenomics analysis context. Together, the two pipelines offer researchers flexible, scalable, and portable pipelines for reproducible metagenomic classifications applicable to any area of microbiology.
Karolinska Institutet