{"id":61,"date":"2014-08-04T19:15:00","date_gmt":"2014-08-04T23:15:00","guid":{"rendered":"https:\/\/med.sites.unc.edu\/microimm\/dittmerlab\/dittmerlab\/downloads\/software\/"},"modified":"2018-03-15T10:58:12","modified_gmt":"2018-03-15T14:58:12","slug":"software","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/downloads\/software\/","title":{"rendered":"Software"},"content":{"rendered":"<p><!-- description --><\/p>\n<p>Open-Source Software developed in-house<\/p>\n<h2>Vironator<\/h2>\n<p>Vironator is a virus-hunting program. It uses a novel classification algorithm with Radial Distance Weighted Discrimination, to classify real-life samples as positive or negative matches. Its training stage allows it to detect non-identical but related targets, as well as detecting target within a specific background (e.g. detecting specific virus in Human with bacterial infection). Vironator is developed by Jie Xiong and Jordan Texier.<\/p>\n<p>Requirements:<\/p>\n<ul>\n<li>MATLAB 2013a<\/li>\n<li>Bowtie2<\/li>\n<li>Samtools<\/li>\n<\/ul>\n<p>Downloads: <strong>TBA<\/strong><\/p>\n<p>(will be available to download after publication)<\/p>\n<h2>Prime Time<\/h2>\n<p>PrimeTime is our in-house software for high throughput primer design. It is available free only for academic and non-commercial uses. Any use requires attribution of the original work [Dongmei Yang, Wolfgang Vahrson and Dirk P. Dittmer &#8211; paper citation TBA]. If you want to use PrimeTime for commercial purpose, you need to license it separately from these authors. Note: No warranty or fitness of any kind is implied. This is research code!<\/p>\n<div class = \"alert alert-warning  oscitas-bootstrap-container\">\nWarning: The following code is optimized for OSX 10.5 and MySQL 5.0. These versions are now obsolete. Use with care:<br \/>\n<\/div>\nDownload the source code: <a title=\"\" href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-content\/uploads\/sites\/606\/2018\/03\/PrimeTime.zip\" target=\"_self\">PrimeTime version 0.1<\/a><br \/>\nDownload the pre-built and easy-to-install package: <a title=\"\" href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-content\/uploads\/sites\/606\/2018\/03\/PrimeTimeBuild.zip\" target=\"_self\">PrimeTime Package<\/a><\/p>\n<h2>\u00a0Vivonatev<\/h2>\n<p>Vivonatev is a NGS mapping pipeline using Bowtie2 and Samtools. This pipeline can match NGS reads to large amounts of reference genomes. Features include:<\/p>\n<ul>\n<li>Can map both single-end and paired-end NGS reads<\/li>\n<\/ul>\n<ul>\n<li>Ability to recursively filter out each reference genome<\/li>\n<\/ul>\n<ul>\n<li>Extract positively mapped reads<\/li>\n<\/ul>\n<ul>\n<li>Generate coverage vector of each genome<\/li>\n<\/ul>\n<ul>\n<li>Threshold for filtering and generating coverage vector (saves a lot of time)<\/li>\n<\/ul>\n<div class = \"alert alert-success  oscitas-bootstrap-container\">\nPrerequisites: Bowtie2, Samtools, bam2fastq (from Hudson Alpha), python 2.7<br \/>\n<\/div>\n<p>Download from Github Repository: <a title=\"\" href=\"https:\/\/github.com\/jrtex\/vivonatev\" target=\"_self\">Vivonatev<\/a><\/p>\n<p>Direct Download: <a title=\"\" href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-content\/uploads\/sites\/606\/2018\/03\/vivonatev.tar_.gz\" target=\"_self\">tar.gz<\/a><\/p>\n<p>Direct Download: <a title=\"\" href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-content\/uploads\/sites\/606\/2018\/03\/vivonatev.zip\" target=\"_self\">zip<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Open-Source Software developed in-house Vironator Vironator is a virus-hunting program. It uses a novel classification algorithm with Radial Distance Weighted Discrimination, to classify real-life samples as positive or negative matches. Its training stage allows it to detect non-identical but related targets, as well as detecting target within a specific background (e.g. detecting specific virus in &hellip; <a href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/downloads\/software\/\" aria-label=\"Read more about Software\">Read more<\/a><\/p>\n","protected":false},"author":8147,"featured_media":0,"parent":15,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-61","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/pages\/61","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/users\/8147"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/comments?post=61"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/pages\/61\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/pages\/15"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/wp-json\/wp\/v2\/media?parent=61"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}