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@@ -4,7 +4,7 @@ This repository contains a conda environment and Snakemake pipeline to bioinform
## Overview
MetaWorks comes with a conda environment file MetaWorks_v1 that should be activated before running the pipeline. An additional program, the RDP classifier v2.12 should also be installed and it is available from https://sourceforge.net/projects/rdp-classifier . If pseudogene filtering will be used, then the NCBI ORFfinder program will also need to be installed and it is available from https://www.ncbi.nlm.nih.gov/orffinder . Additional instructions for installing and using conta, downloading and installing the RDP classifier and ORFfinder are available below under Implementation Notes.
MetaWorks comes with a conda environment file MetaWorks_v1 that should be activated before running the pipeline. An additional program, the RDP classifier v2.12 should also be installed and it is available from https://sourceforge.net/projects/rdp-classifier . If pseudogene filtering will be used, then the NCBI ORFfinder program will also need to be installed and it is available from https://www.ncbi.nlm.nih.gov/orffinder . Additional instructions for installing and using conda, downloading and installing the RDP classifier and ORFfinder are available below under Implementation Notes.
Snakemake requires three sets of data to run: a directory containing the raw paired-end Illumina sequence files (fastq.gz), a configuration file, and the snakefile itself that describes the pipeline.
