{"repo":"replikation/poreCov","free":true,"listed":false,"github":"https://github.com/replikation/poreCov","clone":"git clone https://github.com/replikation/poreCov.git","description":"SARS-CoV-2 workflow for nanopore sequence data","language":"Nextflow","stars":42,"topics":["workflow","nanopore-data","artic","bioinformatics","sars-cov-2","nanopore","basecalling"],"license":"GPL-3.0","category":"workflow-automation","readme_excerpt":"poreCov SARS-CoV-2 Workflow for nanopore sequencing data === Citation: poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer https://www.frontiersin.org/articles/10.3389/fgene.2021.711437/full What is this Repo? poreCov is a SARS-CoV-2 analysis workflow for nanopore data (via the ARTIC protocol) or SARS-CoV-2 genomes (fasta) the workflow is pre-configured to simplify data analysis: Table of Contents ================= - poreCov SARS-CoV-2 Workflow for nanopore sequencing data - What is this Repo? - Table of Contents - 1. Quick Setup (Ubuntu) - 1.1 Nextflow (the workflow manager) - 1.2 Container (choose one - they manage all the tools) - Docker - Singularity - Conda (not recommended) - 1.3 Basecalling (optional) - 2. Run poreCov - 2.1 Test run - 2.2 Quick run examples - 2.3 Extended Usage - Version control - Important input flags (choose one) - Custom primer bed files - Sample input - Sample sheet - List input - Pangolin Lineage definitions - 3. Quality Metrics (default) - 4. Workflow - 5. Literature / References to cite - 6. Troubleshooting - Singularity - 7. Time to results - 8. Credits 1. Quick Setup (Ubuntu) 1.1 Nextflow (the workflow manager) poreCov needs Nextflow and java run time (default-jre) install java run time via: sudo apt install -y default-jre install Nextflow via: curl -s https://get.nextflo","default_branch":null,"files":null,"tree":[],"storefront":"/r/replikation","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/replikation/poreCov/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."}