{"repo":"EBI-Metagenomics/emg-viral-pipeline","free":true,"listed":false,"github":"https://github.com/EBI-Metagenomics/emg-viral-pipeline","clone":"git clone https://github.com/EBI-Metagenomics/emg-viral-pipeline.git","description":"VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies","language":"Python","stars":153,"topics":["nextflow","viruses","cwl","workflow","pipeline"],"license":"Apache-2.0","category":"workflow-automation","readme_excerpt":"1. The VIRify pipeline 2. Nextflow execution 3. Pipeline overview 4. Detour: Metatranscriptomics 5. Frequently Asked Questions (FAQ) 6. Resources 7. Technical Details 8. Citations VIRify General VIRify is a pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify's taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,013 orthologous protein domains and referred to as ViPhOGs. The pipeline is implemented in Nextflow and additionally only Docker or Singularity are needed to run VIRify. Details about installation and usage are given below. Nextflow A Nextflow implementation of the VIRify pipeline. What do I need? This implementation of the pipeline runs with the workflow manager Nextflow and needs as second dependency either Docker or Singularity. Conda will be implemented soonish, hopefully (currently blocked bc/ we use PPR-Meta). However, we highly recommend in any way the usage of the stable containers. All other programs and databases are automatically downloaded by Nextflow. Attention , the workflow will download the containers and databases with a size of roughly 19 GB (49 GB with --hmmextend and --blastextend ) the first time it is executed! Install Nextflow for troubleshooting, see more instructions about Nextflow. Install Docker If you","default_branch":null,"files":null,"tree":[],"storefront":"/r/EBI-Metagenomics","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/EBI-Metagenomics/emg-viral-pipeline/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}