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1 ***Virana***
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3 **The Virus Analysis Toolkit**
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5 Virana, the virus analysis toolkit, is a Python-based software toolkit for analyzing metatranscriptomic (and, to a degree, metagenomic) sequence data in a context of clinical metagenomics in order to:
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7 - identify pathogen nucleotide sequences in transcriptomic (and, while less tested, genomic) short read data
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8 - identify pathogen transcripts diverged from known references of various microbial species
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9 - identify transcripts expressed at low abundances across multiple samples
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10 - identify transcripts homologous to human factors such as certain viral oncogenes
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12 A recent analysis of human tumor transcriptomes displays the ability of Virana to detect diverged viral nucleotide sequences and human-viral homologs with high sensitivity.
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13 The manuscript is available at doi:10.1371/journal.pcbi.1003228 and http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003228
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16 **Licence**
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18 For licence information see https://github.com/schelhorn/virana/raw/master/LICENSE
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21 **Installation**
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23 Using the virana tool shed repository, all dependencies are installed automatically.
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26 **Usage**
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28 There is an example workflow in the virana tool shed repository. Feel free to import the workflow and get familiar with the usage of the toolkit.
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