{"id":280,"date":"2022-08-09T09:59:56","date_gmt":"2022-08-09T13:59:56","guid":{"rendered":"https:\/\/research.ncsu.edu\/gsl\/?page_id=280"},"modified":"2022-12-01T09:03:07","modified_gmt":"2022-12-01T14:03:07","slug":"bioinformatic-resources","status":"publish","type":"page","link":"https:\/\/research.ncsu.edu\/gsl\/bioinformatic-resources\/","title":{"rendered":"Bioinformatic Resources"},"content":{"rendered":"\n<p><strong>Disclaimer<\/strong>&nbsp;\u2013 The following public and NC State resources are listed for help in bioinformatic analysis, and are meant to be a resource guide for the greater research community. It is worth noting, however, that use of these resources, without full knowledge of the appropriate procedures and necessary experimental designs, could lead to misleading or spurious results. The GSL highly recommends consultation with the NCSU&nbsp;<a href=\"http:\/\/brc.ncsu.edu\/consulting\" target=\"_blank\" rel=\"noreferrer noopener\">Bioinformatic Consulting &amp; Service Core<\/a>, who can provide a free initial consultation for first time users upon request.<\/p>\n\n\n\n<p><strong>NC State University also has an active Bioinformatics Users Group that offers a&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/groups.google.com\/a\/ncsu.edu\/g\/group-bioinformatics-users\" target=\"_blank\">Google Group<\/a>&nbsp;for questions and discussion, a&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/github.ncsu.edu\/lllowe\/BioinformaticsUsersGroup\" target=\"_blank\">Github repository<\/a>&nbsp;for scripts, tutorials and other resources, and a shared&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/drive.google.com\/drive\/folders\/0AC1DHkNrcTEnUk9PVA\" target=\"_blank\">Google Drive folder<\/a>&nbsp;for sample datasets, papers, and documentation.<\/strong><\/p>\n\n\n<hr>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"autoheading-0\">Consulting &amp; Data Analysis<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong><a href=\"http:\/\/brc.ncsu.edu\/consulting\" target=\"_blank\" rel=\"noreferrer noopener\">NCSU Bioinformatic Consulting &amp; Service Core<\/a>&nbsp;\u2013&nbsp;<\/strong>The&nbsp;<a href=\"http:\/\/brc.ncsu.edu\/consulting\" target=\"_blank\" rel=\"noreferrer noopener\">BCSC<\/a>&nbsp;offers expertise in analysis of data related to genetics and genomics. Services are available to all members of the North Carolina State University community, as well as the research community at large.<\/li>\n<\/ul>\n\n\n<hr>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"autoheading-1\">Learning Resources<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Select NCSU Courses (many great courses available)<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/wolfware.ncsu.edu\/courses\/details\/?sis_id=SIS:2021:8:1:GN:427:001\">GN 427 (Introductory Bioinformatics)<\/a>&nbsp;\u2013 Dr. David Reif<\/li>\n\n\n\n<li><a href=\"https:\/\/biotech.ncsu.edu\/files\/2020\/03\/BIT815_DSA_Sept2017.pdf\">BIT 815 (Deep Sequencing Analysis)<\/a>&nbsp;\u2013 Dr. Ross Whetten; see&nbsp;<strong><a href=\"https:\/\/deepseqanalysis.readthedocs.io\/en\/latest\/\">Course Webpage<\/a><\/strong><\/li>\n\n\n\n<li><a href=\"https:\/\/biotech.ncsu.edu\/files\/2020\/03\/BIT477_577-Metagenomics_slide.pdf\">BIT 477\/577 (Metagenomics)<\/a>&nbsp;\u2013 Dr. Carlos Goller; see Metagenomics Course&nbsp;<strong><a href=\"https:\/\/metagenomics.pressbooks.com\/\">Pressbook<\/a><\/strong><\/li>\n\n\n\n<li><a href=\"https:\/\/wolfware.ncsu.edu\/courses\/details\/?sis_id=SIS:2022:1:1:ST:590:001\">ST590 (Bioinformatics II)<\/a>&nbsp;\u2013 Dr. Jeffrey Thorne<\/li>\n\n\n\n<li><a href=\"https:\/\/biotech.ncsu.edu\/spring-2022\/bit-495-595-comparative-plant-transcriptomics\/\">BIT 495\/595 (Comparative Plant Transcriptomics)<\/a>&nbsp;\u2013 Dr. Carly Sjogren<\/li>\n\n\n\n<li><a href=\"https:\/\/wolfware.ncsu.edu\/courses\/details\/?sis_id=SIS:2021:8:1:AEC:510:001\">AEC 510 (Machine Learning Approaches for Biological Sciences)<\/a>&nbsp;\u2013 Dr. Benjamin Reading<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Mini-Courses<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/brc.ncsu.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">NCSU BRC Short Courses<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.coursera.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Coursera<\/a>&nbsp;\u2013 Bioconductor for Genomic Data Sciences, Genomic Data Sciences with Galaxy, Command Line Tools for Genomic Data Analysis<\/li>\n\n\n\n<li><a href=\"https:\/\/www.edx.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Edx<\/a>&nbsp;\u2013 ChIP-seq data analysis, RNA-seq data analysis, DNA methylation data analysis<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Other References<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"http:\/\/a-little-book-of-r-for-bioinformatics.readthedocs.org\/en\/latest\/\" target=\"_blank\">The Little Book of R for Bioinformatics<\/a><\/li>\n\n\n\n<li><a rel=\"noreferrer noopener\" href=\"http:\/\/manuals.bioinformatics.ucr.edu\/home\/R_BioCondManual\" target=\"_blank\">R &amp; Bioconductor Manual<\/a><\/li>\n<\/ul>\n\n\n<hr>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"autoheading-2\">Hardware Resources<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">NCSU Users<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/www.ncsu.edu\/hpc\/About\/Services.php\" target=\"_blank\" rel=\"noreferrer noopener\">OIT High Performance Computing&nbsp;<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/brcwebportal.cos.ncsu.edu\/cluster_workshop\/doku.php\" target=\"_blank\" rel=\"noreferrer noopener\">BRC Computing<\/a>&nbsp;(controlled access)<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Public Access<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/www.cyverse.org\/\">CyVerse<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/usegalaxy.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Galaxy<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/www.phylo.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">CIPRES&nbsp;<\/a>(phylogenetics)<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Fee for Use<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/aws.amazon.com\/ec2\/\" target=\"_blank\" rel=\"noreferrer noopener\">Amazon Elastic Compute Cloud&nbsp;<\/a>(EC2)<\/li>\n<\/ul>\n\n\n<hr>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"autoheading-3\">Software Resources<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">NCSU Users<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/www.ncsu.edu\/hpc\/Software\/Software.php\" target=\"_blank\" rel=\"noreferrer noopener\">OIT High Performance Computing<\/a>&nbsp;\u2013 IBM Blade Center Linux Cluster (henry2) with LSF job submission. MAKER genome annotation, PBJelly, Trinity, Velvet\/Oases, SOAPdenovo2, MrBayes, FastXToolkit, Bowtie2, TopHat, Cufflinks, GenomeTools, SAMTools, PacBio SMRT analysis, and much more!<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Open Access\/Freeware<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.bioconductor.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Bioconductor<\/a>&nbsp;\u2013 An R-based statistical platform for analyzing high-throughput genomic data.<\/li>\n\n\n\n<li><a href=\"http:\/\/www.cyverse.org\/\">CyVerse Discovery Environment<\/a>&nbsp;\u2013 BLAST\/BLAT, BEDtools, CEGMA, MetaGeneMark, InterProScan, BWA, Bowtie, SAMTools, FastX toolkit, GBS workflows, and much more!<\/li>\n\n\n\n<li><a href=\"https:\/\/usegalaxy.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Galaxy<\/a>&nbsp;\u2013 FastQC, FastQ conversions, Bowtie2, BWA, Tophat, Cufflinks, Cuffdiff, SAMtools, BAMtools, and much more!<\/li>\n\n\n\n<li><a href=\"http:\/\/www.phylo.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">CIPRES<\/a>&nbsp;\u2013 RAxML; MrBayes; BEAST; BEAST2; GARLI; MAFFT; DPPDIV; FastTree, jModelTest2, Migrate-N, PAUP*, Poy, ClustalW, Contralign, MUSCLE, PROBCONS, PROBALIGN<\/li>\n\n\n\n<li><a href=\"http:\/\/ugene.unipro.ru\/\" target=\"_blank\" rel=\"noreferrer noopener\">UGENE<\/a>&nbsp;\u2013 Free Java-based NGS pipeline for variant calling, RNA-seq, and ChIP-seq data analysis.<\/li>\n\n\n\n<li><a href=\"http:\/\/www.cs.waikato.ac.nz\/ml\/weka\/\" target=\"_blank\" rel=\"noreferrer noopener\">WEKA<\/a>&nbsp;\u2013 Open-source machine-learning algorithms for data mining.<\/li>\n\n\n\n<li><a href=\"https:\/\/david.ncifcrf.gov\/tools.jsp\" target=\"_blank\" rel=\"noreferrer noopener\">DAVID<\/a>&nbsp;\u2013 Online gene-enrichment and functional pathway analysis tool.<\/li>\n\n\n\n<li><a href=\"http:\/\/www.mothur.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">MOTHUR<\/a>&nbsp;\u2013 Open-source software for microbial ecology and metagenomics.<\/li>\n\n\n\n<li><a href=\"https:\/\/metagenomics.anl.gov\/\" target=\"_blank\" rel=\"noreferrer noopener\">MG-RAST&nbsp;<\/a>\u2013 An automated analysis platform for metagenomics.<\/li>\n\n\n\n<li><a href=\"http:\/\/qiime.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">QIIME<\/a>&nbsp;\u2013 A bioinformatics pipeline for performing microbiome analysis.<\/li>\n\n\n\n<li><a href=\"https:\/\/en.wikipedia.org\/wiki\/List_of_open-source_bioinformatics_software\" target=\"_blank\" rel=\"noreferrer noopener\">Open-Source List<\/a>&nbsp;\u2013 A general list of open-source bioinformatics software packages.<\/li>\n\n\n\n<li><a href=\"http:\/\/www.usadellab.org\/cms\/index.php?page=trimmomatic\" target=\"_blank\" rel=\"noreferrer noopener\">Trimmomatic<\/a>&nbsp;\u2013 A flexible read trimming tool for Illumina NGS data.<\/li>\n\n\n\n<li><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/\" target=\"_blank\" rel=\"noreferrer noopener\">FastQC<\/a>&nbsp;\u2013 A Java based software for assessing read quality<\/li>\n\n\n\n<li><a href=\"https:\/\/nephele.niaid.nih.gov\/#home\">Nephele<\/a>&nbsp;\u2013 NIH supported microbiome analysis pipeline&nbsp;<strong>\u2013 NEW!<\/strong><\/li>\n\n\n\n<li><a href=\"https:\/\/www.onecodex.com\/\">One Codex<\/a>&nbsp;\u2013 data platform for applied microbial genomics&nbsp;<strong>\u2013 NEW!<\/strong><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Disclaimer&nbsp;\u2013 The following public and NC State resources are listed for help in bioinformatic analysis, and are meant to be a resource guide for the greater research community. It is&hellip;<\/p>\n","protected":false},"author":1127,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"ncst_custom_author":"","ncst_show_custom_author":false,"ncst_dynamicHeaderBlockName":"ncst\/floating-box-header","ncst_dynamicHeaderData":"{\"backgroundColor\":\"red_400\",\"boxPosition\":\"left\",\"ctaNum\":\"one\",\"imageID\":54,\"imageURL\":\"https:\/\/research.ncsu.edu\/gsl\/files\/2022\/07\/about-dna.jpg\",\"imageAlt\":\"blue dna\"}","ncst_content_audit_freq":"","ncst_content_audit_date":"","ncst_content_audit_display":false,"ncst_backToTopFlag":"","footnotes":""},"tags":[],"class_list":["post-280","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Bioinformatic Resources - Genomic Sciences Laboratory<\/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:\/\/research.ncsu.edu\/gsl\/bioinformatic-resources\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Bioinformatic Resources - Genomic Sciences Laboratory\" \/>\n<meta property=\"og:description\" content=\"Disclaimer&nbsp;\u2013 The following public and NC State resources are listed for help in bioinformatic analysis, and are meant to be a resource guide for the greater research community. 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