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Our IVAR shelving units are old dogs that love new tricks. We’ve been developing them for more than 50 years. They’re one of our favourite customisable shelving systems because they can easily be stylish showstoppers and storage superheroes. Browse our combinations to see what IVAR can do for you!
- Overview
- Insallation
- Installing via conda
- Installing build tools
- HTSlib installed using conda
- HTSlib installed from source
- Installing iVar
- Running from Docker
- GeneratedCaptionsTabForHeroSec
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Genome Biology 2019 20:8
Nathan D Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L Matteson, Jaqueline Goes De Jesus, Bradley J Main, Amanda L Tan, Lauren M Paul, Doug E Brackney, Saran Grewal, Nikos Gurfield, Koen KA Van Rompay, Sharon Isern, Scott F Michael, Lark L Coffey, Nicholas J Loman, Kristian G Andersen
Dependencies
•HTSlib •GCC any version after v5.0. Support for C++11 standard required. Note: •It is highly recommended that samtools also be installed alongside iVar. iVar uses the output of samtools mpileup to call variants and generate consensus sequences. In addition, samtools sort and index commands are very useful to setup a pipeline using iVar.
iVar is available on bioconda. To install conda, please use the miniconda package. After intalling conda please add the following channels,
To install iVar,
Xcode from Apple is required to compile iVar (and other tools) from source. If you don't want to install the full Xcode package from the AppStore, you can install the Xcode command line tools,
GNU Autotools is required to compile iVar from source.
HTSlib can be installed with conda using the command,
The conda binary is by default installed at /opt/. You can check the installation location by running the following command,
The output of the command will be in this format - /opt/conda/bin/conda or /opt/anaconda2/bin/conda or /opt/anaconda3/bin/conda depending on whether you installed miniconda or anaconda.
If the output is for example, /opt/conda/bin/conda, then you can add the path to the lib folder to $LD_LIBRARY_PATH using the command below. You can add this to your ~/.bash_profile or ~/.bashrc to avoid rerunning the command everytime a new bash session starts.
Installation instructions and downloads for HTSlib can be found at http://www.htslib.org/download/.
If HTSlib is installed in a non standard location, please add the following to your .bash_profile so that iVar can find HTSlib dynamic libraries during runtime.
To install iVar, run the following commands.
If HTSlib was installed using conda, please run the following commands by supplying the prefix to the bin folder of the conda binary.
The prefix to the bin folder can be found using the command which conda. The output of the command will be in this format - /opt/conda/bin/conda or /opt/anaconda2/bin/conda or /opt/anaconda3/bin/conda depending on whether you installed miniconda or anaconda. For example, if the output of the command is /opt/conda/bin/conda, the prefix to the htslib bin folder will be /opt/conda. This can be supplied to ./configure --with-hts=/opt/conda.
If HTSlib was installed in a non standard location, please run the following commands,
iVar can also be run via Docker. Pull the docker image from Docker Hub using the following command,
This docker image contains all the required dependencies to run iVar and the [pipelines](@ref cookbookpage) developed using iVar. You will have to attach a docker volume to get data into the docker container. Instructions to do so are in the Docker docs.
iVar is a tool for trimming, consensus calling, variant calling and mismatch filtering of viral sequencing data. It is available on bioconda, homebrew and source installation, and requires HTSlib and GCC.
May 9, 2024 · Ivar the Boneless (died 873, Dublin [Ireland]) was a Viking chieftain, of Danish origin, whose life story is suffused with legend. He is best known for his exploits on the British Isles, most notably his invasion, in the company of two brothers, of several Anglo-Saxon kingdoms.
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Ivar the Boneless ( Old Norse: Ívarr hinn Beinlausi [ˈiːˌwɑrː ˈhinː ˈbɛinˌlɔuse]; died c. 873), also known as Ivar Ragnarsson, was a Viking leader who invaded England and Ireland.
IVAR is a versatile and durable storage system that can be customized to suit your space and style. It is available in various sizes and colors, and can be combined with other IKEA products.
Mar 7, 2016 · This is my full setup of the IVAR Wall System from IKEA. It took me about a 90 minutes to do by myself. I'm sure with one extra set of hands it would have be...
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