{"id":51,"date":"2015-11-06T19:45:00","date_gmt":"2015-11-07T00:45:00","guid":{"rendered":"https:\/\/med.sites.unc.edu\/microimm\/dittmerlab\/dittmerlab\/about-us\/bioinformatics-hardware-software\/"},"modified":"2020-08-27T12:18:00","modified_gmt":"2020-08-27T16:18:00","slug":"bioinformatics-hardware-software","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/about-us\/bioinformatics-hardware-software\/","title":{"rendered":"Bioinformatics Hardware\/Software"},"content":{"rendered":"<p class=\"lead\">See the machines used in the lab below, as well as their installed software.<\/p>\n<h3>Tempest 4400 Computing Server<\/h3>\n<table class=\"table table-hover\" border=\"0\">\n<tbody>\n<tr>\n<th><strong>CPU<\/strong><\/th>\n<th><strong>RAM<\/strong><\/th>\n<th><strong>GPU<\/strong><\/th>\n<th><strong>Storage<\/strong><\/th>\n<th><strong>OS <\/strong><\/th>\n<\/tr>\n<tr>\n<td><span class=\"smallFont\">4x AMD Opteron 6376 16C\/2.3GHz<\/span><\/td>\n<td><span class=\"smallFont\">256 GB ECC<\/span><\/td>\n<td><span class=\"smallFont\">Nvidia Quadro FX3800 1GB<\/span><\/td>\n<td><span class=\"smallFont\">30 TB RAID6<\/span><\/td>\n<td><span class=\"smallFont\">CentOS 7.1<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h4>Software<\/h4>\n<table style=\"border-collapse: collapse;width: 100%\">\n<tbody>\n<tr>\n<th><strong><a href=\"https:\/\/github.com\/shenwei356\/seqkit\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">seqkit<\/span><\/a><\/strong><\/th>\n<th><strong><a href=\"http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">FASTX toolkit<\/span><\/a><\/strong><\/th>\n<th colspan=\"2\"><strong><a href=\"http:\/\/www.454.com\/products\/analysis-software\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">GS <i>de novo<\/i> assembler (Newbler)<\/span><\/a><\/strong><\/th>\n<\/tr>\n<tr>\n<td><a href=\"http:\/\/qiime.org\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">QIIME<\/span><\/a><\/td>\n<td><a href=\"https:\/\/github.com\/csmiller\/EMIRGE\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">EMIRGE<\/span><\/a><\/td>\n<td><a href=\"https:\/\/en.wikipedia.org\/wiki\/Just_another_Gibbs_sampler\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">JAGS<\/span><\/a><\/td>\n<td><span class=\"smallFont\"><a href=\"https:\/\/www.rstudio.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Rstudio<\/a> Server<\/span><\/td>\n<td><span class=\"smallFont\"><a href=\"https:\/\/www.rstudio.com\/products\/shiny\/shiny-server\/\" target=\"_blank\" rel=\"noopener noreferrer\">Shiny<\/a> Server<\/span><\/td>\n<td><a href=\"https:\/\/github.com\/samtools\/samtools\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">Samtools<\/span><\/a><\/td>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/github.com\/BenLangmead\/bowtie2\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">Bowtie2<\/span><\/a><\/td>\n<td><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Traces\/sra\/sra.cgi?cmd=show&amp;f=software&amp;m=software&amp;s=software\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">SRA Toolkit<\/span><\/a><\/td>\n<td><a href=\"http:\/\/repeatmasker.org\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">repeatmasker<\/span><\/a><\/td>\n<td><a href=\"https:\/\/www.drive5.com\/usearch\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">USEARCH<\/span><\/a><\/td>\n<td><a href=\"http:\/\/www.cbcb.umd.edu\/software\/jellyfish\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">jellyfish<\/span><\/a><\/td>\n<td><a href=\"ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/LATEST\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">BLAST<\/span><\/a><\/td>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/github.com\/kylebittinger\/brocc\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">brocc<\/span><\/a><\/td>\n<td><a href=\"https:\/\/jgi.doe.gov\/data-and-tools\/bbtools\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">bbmap<\/span><\/a><\/td>\n<td><a href=\"http:\/\/bioinf.spbau.ru\/spades\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">SPAdes<\/span><\/a><\/td>\n<td><a href=\"http:\/\/www.chevreux.org\/projects_mira.html\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">Mira<\/span><\/a><\/td>\n<td><a href=\"https:\/\/github.com\/eclarke\/sunbeam\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">Sunbeam<\/span><\/a><\/td>\n<td><a href=\"http:\/\/hmmer.janelia.org\/\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">hmmer<\/span><\/a><\/td>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/github.com\/ekg\/freebayes\" target=\"_blank\" rel=\"noopener noreferrer\"><span class=\"smallFont\">freebayes<\/span><\/a><\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Mac Pro 2013 (1)<\/h3>\n<table class=\"table table-hover\" border=\"0\">\n<tbody>\n<tr>\n<th><strong>CPU<\/strong><\/th>\n<th><strong>RAM<\/strong><\/th>\n<th><strong>GPU<\/strong><\/th>\n<th><strong>Storage<\/strong><\/th>\n<th><strong>Other<\/strong><\/th>\n<\/tr>\n<tr>\n<td><span class=\"smallFont\">Intel Xeon E5 8C 3GHz<\/span><\/td>\n<td><span class=\"smallFont\">64 GB<\/span><\/td>\n<td><span class=\"smallFont\">AMD Firepro D500 3GB<\/span><\/td>\n<td><span class=\"smallFont\">1 TB PCie SSD<\/span><\/td>\n<td><span class=\"smallFont\">28 TB External Storage<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h4>Software<\/h4>\n<ul>\n<li><span class=\"smallFont\"><a href=\"http:\/\/www.clcbio.com\/products\/clc-genomics-workbench\/\" target=\"_blank\" rel=\"noopener noreferrer\">CLC Genomics Workbench<\/a><\/span><\/li>\n<li><span class=\"smallFont\"><a href=\"http:\/\/www.geneious.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">Geneious<\/a><\/span><\/li>\n<li><span class=\"smallFont\">MATLAB 2015a<\/span><\/li>\n<li><span class=\"smallFont\">Rstudio<\/span><\/li>\n<li><span class=\"smallFont\"><a href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/downloads\/software\" target=\"_blank\" rel=\"noopener noreferrer\">Vironator<\/a><\/span><\/li>\n<\/ul>\n<h3>Mac Pro 2013 (2)<\/h3>\n<table class=\"table table-hover\" border=\"0\">\n<tbody>\n<tr>\n<th><strong>CPU<\/strong><\/th>\n<th><strong>RAM<\/strong><\/th>\n<th><strong>GPU<\/strong><\/th>\n<th><strong>Storage<\/strong><\/th>\n<\/tr>\n<tr>\n<td><span class=\"smallFont\">Intel Xeon E5 8C 3GHz<\/span><\/td>\n<td><span class=\"smallFont\">64 GB<\/span><\/td>\n<td><span class=\"smallFont\">AMD Firepro D500 3GB<\/span><\/td>\n<td><span class=\"smallFont\">1 TB PCie SSD<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h4>Software<\/h4>\n<ul>\n<li><span class=\"smallFont\"><a href=\"http:\/\/www.bitplane.com\/imaris\/imaris\" target=\"_blank\" rel=\"noopener noreferrer\">Imaris<\/a> Core<\/span><\/li>\n<\/ul>\n<h3>Mac Pro 2012<\/h3>\n<table class=\"table table-hover\" border=\"0\">\n<tbody>\n<tr>\n<th><strong>CPU<\/strong><\/th>\n<th><strong>RAM<\/strong><\/th>\n<th><strong>GPU<\/strong><\/th>\n<th><strong>Storage<\/strong><\/th>\n<th><strong>Other<\/strong><\/th>\n<\/tr>\n<tr>\n<td><span class=\"smallFont\">2x &#8211; Intel Xeon 6C 3GHz<\/span><\/td>\n<td><span class=\"smallFont\">64 GB<\/span><\/td>\n<td><span class=\"smallFont\">ATI Radeon HD5870 1GB<\/span><\/td>\n<td><span class=\"smallFont\">2TB RAID 0 SSD<\/span><\/td>\n<td><span class=\"smallFont\">12 TB External Storage<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h4>Software<\/h4>\n<ul>\n<li><span class=\"smallFont\">Bowtie2<\/span><\/li>\n<li><span class=\"smallFont\">CLC Genomics Workbench<\/span><\/li>\n<li><span class=\"smallFont\">MATLAB 2015a<\/span><\/li>\n<li><span class=\"smallFont\">Rstudio<\/span><\/li>\n<li><span class=\"smallFont\"><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Sequin\/\" target=\"_blank\" rel=\"noopener noreferrer\">Sequin<\/a><\/span><\/li>\n<li><span class=\"smallFont\">Vironator<\/span><\/li>\n<\/ul>\n<h3>Mac Pro 2010<\/h3>\n<table class=\"table table-hover\" border=\"0\">\n<tbody>\n<tr>\n<th><strong>CPU<\/strong><\/th>\n<th><strong>RAM<\/strong><\/th>\n<th><strong>GPU<\/strong><\/th>\n<th><strong>Storage<\/strong><\/th>\n<th><strong>Other<\/strong><\/th>\n<\/tr>\n<tr>\n<td><span class=\"smallFont\">2x &#8211; Intel Xeon 6C 2.7GHz<\/span><\/td>\n<td><span class=\"smallFont\">48 B<\/span><\/td>\n<td><span class=\"smallFont\">ATI Radeon HD5770 1GB<\/span><\/td>\n<td><span class=\"smallFont\">1TB RAID 0 SSD<\/span><\/td>\n<td><span class=\"smallFont\">4TB External Storage<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h4>Software<\/h4>\n<ul>\n<li><span class=\"smallFont\">CLC Genomics Workbench<\/span><\/li>\n<li><span class=\"smallFont\">Rstudio<\/span><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Tempest 4400 Computing Server CPU RAM GPU Storage OS 4x AMD Opteron 6376 16C\/2.3GHz 256 GB ECC Nvidia Quadro FX3800 1GB 30 TB RAID6 CentOS 7.1 Software seqkit FASTX toolkit GS de novo assembler (Newbler) QIIME EMIRGE JAGS Rstudio Server Shiny Server Samtools Bowtie2 SRA Toolkit repeatmasker USEARCH jellyfish BLAST brocc bbmap SPAdes Mira Sunbeam &hellip; <a href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/about-us\/bioinformatics-hardware-software\/\" aria-label=\"Read more about Bioinformatics Hardware\/Software\">Read more<\/a><\/p>\n","protected":false},"author":8147,"featured_media":0,"parent":6,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-51","page","type-page","status-publish","hentry","odd"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Bioinformatics Hardware\/Software - Dittmer Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.med.unc.edu\/microimm\/dittmerlab\/about-us\/bioinformatics-hardware-software\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Bioinformatics Hardware\/Software - Dittmer Lab\" \/>\n<meta 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