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This NanoMetaPipe wiki is designed to work as a sort of manual which will take you through many or most steps of the metagenomics pipeline. The pipeline is able to take in raw nanopore sequence reads to carry out basecalling OR take in basecalled reads. In either case, basecalled reads are filtered and decontaminated before carrying out de novo metagenome assembly. The reads are also taxonomically classified and the outputs are used to create interactive HTML files. An analysis R script is also included to provide further information on the microbial community of the provided reads. Furthermore, where you are after a specific species/genus, a secondary workflow is provided to carry out HMM confirmation of the target of interest -- given that you are able to provide either a HMM profile or candidate accession codes in order to generate a HMM profile. Currently, this workflow is optimised for use with SSU reads and the SILVA database. It is important to note that while this pipeline automates a lot of commands, it cannot automate everything. The user is necessary to provide initial inputs, file locations, package/tools locations etc. Generally, once the configuration file is complete, the pipeline should go well, however if you want to tweak the script, the vast majority is written in python with some bash and R sub-scripts.