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PSSchacksen authored Jul 11, 2024
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## Requirements
### Hardware requirements
As a general recommendation for running ONT-AmpSeq while producing every possible output, at least 32 threads and 40 GB of memory are advised. These high requirements stem from the multithreading capabilities of the various software and tools used in the pipeline, as well as the need/possibility to handle very large datasets and databases. While the pipeline has been successfully run with 1 thread and as little as 4 GB of memory using smaller datasets `~/ONT-AmpSeq/.test/test_data` and the MiDAS v5.3 [SINTAX database](https://www.midasfieldguide.org/guide/downloads), using large datasets may cause minimap2 to run out of memory. Additionally, loading the general BLAST-formatted [GenBank database](https://www.ncbi.nlm.nih.gov/genbank/) requires ~40 GB of memory. For more details, see [BLAST database formatting](#databases).
As a general recommendation for running ONT-AmpSeq while producing every possible output, at least 32 threads and 40 GB of memory are advised. These high requirements stem from multithreading capabilities of the various software and tools used in the pipeline, as well as the need/possibility to handle very large datasets and databases. While the pipeline has been successfully run with 1 thread and as little as 4 GB of memory using smaller datasets `~/ONT-AmpSeq/.test/test_data` and the MiDAS v5.3 [SINTAX database](https://www.midasfieldguide.org/guide/downloads), using large datasets may cause minimap2 to run out of memory. Additionally, loading the general BLAST-formatted [GenBank database](https://www.ncbi.nlm.nih.gov/genbank/) requires ~40 GB of memory. For more details, see [BLAST database formatting](#databases).

### Software requirements
To run ONT-AmpSeq, Linux OS or Windows Subsystem for Linux (WSL) is required. Installation of software/tools utilised in the workflow is based on, and requires, a package manager system either conda or mamba. This workflow and walkthrough utilises mamba. Using Snakemake, the correct versions of the tools will automatically be installed to ensure version compatibility. However, prior to installing ONT-AmpSeq, mamba and the appropriate mamba environments are required to facilitate the installation of the various utilised tools for both the Snakemake and SnakeDeploy installations. For more details, see [SnakeDeploy installation](#usage-of-ont-ampseq-using-snakedeploy).
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