diff --git a/README.md b/README.md index 0b3213b..64d7318 100644 --- a/README.md +++ b/README.md @@ -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.