- #INTRODUCTION TO CLC GENOMICS WORKBENCH FULL#
- #INTRODUCTION TO CLC GENOMICS WORKBENCH SOFTWARE#
- #INTRODUCTION TO CLC GENOMICS WORKBENCH PROFESSIONAL#
- #INTRODUCTION TO CLC GENOMICS WORKBENCH FREE#
In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. Kravitz, PhDskravitz clcbio.In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E.
#INTRODUCTION TO CLC GENOMICS WORKBENCH PROFESSIONAL#
Professional ServicesDeveloping customized solutionsIntegration with LIMS, workflows, DBBioinformatics Algorithm DevelopmentCloud and Grid IntegrationData Analysis
Targeted Resequencing QCAssessment of targeted sequencing technolog圜overage Statistics for Targeted RegionsVery short schedule, limited bioinformatics staffPlug-in development leveraging CLC tools to automate the process and meet short deadlineQC Report now available as plug-in Tim Stockwell Director of Viral Informatics J. Very accurate SNP calls in areas of deep coverage. CLC didn’t seem to suffer from biased coverage. Why CLC bioTools?CLC handled hybrid sequencing technologies directly Very biased coverage confounded other assemblers that expect random arrival stats.
#INTRODUCTION TO CLC GENOMICS WORKBENCH FULL#
Viral Sequencing at JCVI(See Nadia Fedorova’s Poster!)Amplify and Barcode using SISPA, 454 + Illumina SequencingDepth of coverage sometimes >1000xDe novo Assembly of Consensus for all SegmentsFor each segment:Map reads from each technology independently using best full length reference from NCBI, call variationsUpdate reference with variations confirmed by multiple technologiesMap reads using updated reference and all readsConvert to consed, analyze, order Sanger closure reactionsSource: Jessica Hostetler, Nadia Federova, Tim Stockwell, Danny Katzel Small RNA Analysis(in Beta soon)Identify and filter/trim adapters annotate using mirBASE and other resources- target species of interest Merge/group by mature, precursor/reference Fully integrated with expression analysisĭe Novo AssemblerHuman assembly of 38x Illumina paired-endCLC Quality equivalent to AbyssCLC: 7 hrs, 1 node, 42 Gbof RAMAbyss: 80 hrs, 21 nodes, 336 Gbof RAMMetagenomics AssemblyMETAHIT Dataset MH0041 40M 75bp paired end3 hrs on desktop, 6 Gb RAMHigher N50 and Total Contig Size than Reported
#INTRODUCTION TO CLC GENOMICS WORKBENCH FREE#
Why not use free tools?Are tools free or “free”?Tools vs solutionsTrue cost of ownershipEase of UseTools integrationSupport Swiss Army Knife of NGS AnalysisSDKIntuitive GUITraditional BioinformaticsVisualizationDesktop SolutionsEnterpriseSolutionsHigh PerformanceFile Format ConversionTools IntegrationEpigenomicsTranscriptomicsGenomicsRNA-SeqmiRNARead MappingDe Novo AssemblySNP/DIP DetectionCHIP-Seq Rapid customization and adaptationCLC bio NGS Analysis PlatformCLC Genomics WorkbenchCLC Genomics Server CLC Assembly CellDeveloper SDKEasy to use, Wizard-driven Desktop SoftwareEnterprise solutionHigh performance NGS algorithmsWorkbench and Server Customization Rapid technology change, applications growth Nextgen Sequencing Revolution2010: $6k Human genome ~1 sequencer dayHelp!!Sample PrepAnalysisSequencingScienceīioinformatics ChallengesData Analysis Tools for Biomedical Researchers Kravitz, PhDDirector of Consulting Servicesīefore the Flood2005: $5M Human genome – 19 sequencer years Sample PrepAnalysisSequencingScience CLC bioA Comprehensive Platformfor NGS Data AnalysisSaul A.
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