{"repo":"medvir/VirMet","free":true,"listed":false,"github":"https://github.com/medvir/VirMet","clone":"git clone https://github.com/medvir/VirMet.git","description":"Set of tools for viral metagenomics.","language":"Python","stars":17,"topics":["bioinformatics","bioinformatics-pipeline","genome","miseq","python","viral-database","viral-metagenomics","ncbi","database","bacterial-database"],"license":null,"category":"databases-storage","readme_excerpt":"VirMet ------ VirMet is a software designed to help users running viral metagenomics (mNGS) experiments. For full Documentation, please Read the Docs. VirMet is called with a command-subcommand syntax. All the possible subcommands are: fetch : download all databases update : update viral database index : index all genomes wolfpack : analyze a Miseq run or file covplot : plot coverage for a specific organism Some help can be obtained with virmet -h or simply virmet -h : Run virmet subcommand -h for more help. Installation Bioconda VirMet is available through Bioconda, a channel for the conda package manager. Once conda is installed and the channels are set up, conda install virmet installs the package with all its dependencies. Preparation VirMet contains programs to download and index the genome sequences, instructions here. Running a virus scan Once the fetch and index subcommands have ben run and the databases are downloaded and indexed, users can use Wolfpack , the main subcommand of VirMet. A very simple way to use Wolfpack is the following: virmet wolfpack --run path to run directory With that, sequencing reads are filtered (quality-control), decontaminated, and finally blasted against a (large) set of viral sequences. Virmet Wolfpack provides several outputs that can be found in the output folder virmet output RUN NAME , located at the current working directory. For example, if users have a directory named Exp01 with files: and run , their results will appear into virme","default_branch":null,"files":null,"tree":[],"storefront":"/r/medvir","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/medvir/VirMet/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."}