Mercurial > repos > mzeidler > virana_main
changeset 40:53a6b7a0d10c draft
Uploaded
| author | mzeidler |
|---|---|
| date | Fri, 11 Oct 2013 04:41:55 -0400 |
| parents | 6084c63a69fd |
| children | 5f634ebef569 |
| files | README |
| diffstat | 1 files changed, 12 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/README Mon Oct 07 11:02:18 2013 -0400 +++ b/README Fri Oct 11 04:41:55 2013 -0400 @@ -2,26 +2,30 @@ **The Virus Analysis Toolkit** -Virana is a GNU/Linux toolbox and python library for performing next-generation sequence analyses on viral targets. +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: + + - identify pathogen nucleotide sequences in transcriptomic (and, while less tested, genomic) short read data + - identify pathogen transcripts diverged from known references of various microbial species + - identify transcripts expressed at low abundances across multiple samples + - identify transcripts homologous to human factors such as certain viral oncogenes + +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. +The manuscript is available at doi:10.1371/journal.pcbi.1003228 and http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003228 **Licence** For licence information see https://github.com/schelhorn/virana/raw/master/LICENSE + **Installation** -Using the virana tool shed repository, all dependencies are installed automatically except 'jalview'. -Make sure to copy the jalview directory, contained in the repository, into the <galaxy root>/tool-data/shared/ directory. +Using the virana tool shed repository, all dependencies are installed automatically. -*Manual Installation* - -For manual installation see https://github.com/schelhorn/virana/raw/master/INSTALL **Usage** -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. -We also provide example datasets for testing here https://github.com/schelhorn/virana/raw/master/test_data. +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.