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BaseSpace Sequence HubApps Quick Guide Get a variety of low-cost data analysis apps with BaseSpace Sequence Hubservices. All services and DRAGEN apps are priced in iCredits. Learn more.Quick linksClick on any of the application areas below to quickly view each section.Biomedical and Basic Research – Genetic Analysis Pages 1–3Data Handling, Data Quality Control (QC), and Data Visualization. . . . . . . . . . . . . . . . . . . . . . Page 4Gene Expression and Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Pages 5–6Microbial Genomics and Metagenomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Pages 7–8Biomedical and Basic Research – Genetic AnalysisApp nameSequencing application(s)Key functionalityVendor Whole-exome sequencing Targeted Resequencing AlignmentSmall Variant CallingSomatic Variant CallingSV/CNV CallingCustom Manifest FilesIllumina, Inc. Whole-genome sequencing Whole-exome sequencing AlignmentSmall variant callingCNV callingSomatic variant callingIllumina, Inc. De novo variant calling Novel variant identificationDRAGEN EnrichmentDemo Data LinkDRAGEN GermlineDemo Data LinkDRAGEN JointGenotyping PipelineDemo Data LinkFor Research Use Only. Not for use in diagnostic procedures.Compute Cost: 2 iCredits per node/hrLicense Cost: n/aExample Compute Cost:FASTQ to SNVs only88M reads, 2 x 150 bpAnalysis cost 2.50 iCredits/sampleCompute cost: 7 iCredits per node/hrLicense cost: n/aExample compute cost:FASTQ to SNVs only88M reads, 2 x 150 bpAnalysis cost 2.50 iCredits/sampleIllumina, Inc.Compute cost: 5 iCredits per node/hrLicense cost: n/aExample compute cost:Input: Trio of gVCFs processed withDRAGEN GermlineAnalysis cost 1 iCredits/sample1

Click here to return to page 1Biomedical and Basic Research – Genetic Analysis (continued)App nameSequencing application(s)Key functionalityVendor Whole-genome sequencing Whole-exome sequencing Alignment Somatic variant calling Tumor-normal andtumor-only analysisIllumina, Inc. Whole-genome sequencing Targeted sequencing Alignment Custom reference genome Batch processingBaseSpace Labs Targeted resequencing(AmpliSeq for Illumina) Alignment Small variant calling AnnotationIllumina, Inc. Targeted Resequencing Variant Annotation Variant AnalysisEONE-DIAGNOMICS Genome Center Targeted resequencing(AmpliSeq for Illumina) CNV callingBaseSpace Labs Targeted resequencing(AmpliSeq for Illumina) CNV callingDRAGEN SomaticPipelineDemo Data LinkBWA AlignerDemo Data LinkDNA AmpliconDemo Data Link 1Demo Data Link 2EDGC AnnotatorDemo Data LinkDemo Data LinkFor Research Use Only. Not for use in diagnostic procedures.basespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:0.72M reads, 2 x 150 bpAnalysis cost 2 iCredits/sampleCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:-0.72M reads, 2 x 150 bpAnalysis cost 2 iCredits/samplewww.edgc.com/edgcannotator?lang enCompute Cost: 3 iCredits per node/hrLicense Cost: n/abasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:18M reads, 2 x 150 bpAnalysis cost 1 iCredits/sampleOncoCNV TrainerOncoCNV CallerCompute cost: 5 iCredits per node/hrLicense cost: n/aExample compute cost:4,750M reads, 2 x 150 bpAnalysis cost 13 iCredits/sampleBaseSpace Labsbasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:18M reads, 2 x 150 bpAnalysis cost 1.5 iCredits/sample2

Click here to return to page 1Biomedical and Basic Research – Genetic Analysis (continued)App nameSequencing application(s)Key functionalityVendor Targeted resequencing(AmpliSeq for Illumina) Insertion and deletionbreakpoint detectionBaseSpace Labs Targeted resequencing Low-frequency somaticvariant detectionBaseSpace Labs Illumina, Inc.PindelDemo Data LinkPisces Variant CallerDemo Data Link Targeted resequencingTruSeq AmpliconDemo Data LinkAlignmentSmall variant callingSomatic variant callingAnnotationCustom manifest filesBatch processingbasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:4.1M reads, 2 x 150 bpAnalysis cost 1 iCredits/samplebasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:7M reads, 2 x 150 bpAnalysis cost 3 iCredits/sampleCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:TruSight Myeloid Panel(5000x mean coverage)2.35M reads, 2 x 150 bpAnalysis cost 0.78 iCredits/sample Targeted resequencing(TruSight Tumor 15 Panel) Alignment Variant callingIllumina, Inc. Targeted resequencing(TruSight Tumor 170 Panel) Variant calling SV/CNV calling RNA fusion callingIllumina, Inc. Targeted resequencing(TruSight Tumor 170) Reduce PCR orsequencing errors forrare and low-frequencysomatic variantsBaseSpace LabsTruSight Tumor 15Demo Data LinkCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:TruSight Tumor 15 Panel(5000x mean coverage)733K reads, 2 x 150 bpAnalysis cost 0.35 iCredits/sampleCompute cost: FreeLicense cost: n/aTruSight Tumor 170UMI Error CorrectionDemo Data LinkDemo Data LinkFor Research Use Only. Not for use in diagnostic procedures.basespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:83M reads, 2 x 125 bpAnalysis cost 2.15 iCredits/sample3

Click here to return to page 1Data Handling, Data Quality Control (QC), and Data VisualizationApp nameSequencing application(s)Key functionalityVendor FASTQ manipulation BaseSpace LabsFASTQ Toolkit Data QCSub-samplingAdapter trimmingBase trimmingQuality trimmingRead filtering Base QC profilebasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aBaseSpace Labsbasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aFASTQCDemo Data LinkIntegrative GenomicsViewer Whole-genome sequencingTargeted resequencingChIP-SeqRNA-Seq Genome browser VisualizationsBaseSpace Labs Data import General NGS Imports NGS data fromNCBI Sequence ReadArchive to BaseSpaceSequence Hub using SRAaccession numberBaseSpace Labs Data export General NGS Submission of data toNCBI SRABaseSpace Labs Data QC Comparison of variantcall sets SNV and Indel statisticsBaseSpace LabsSRA ImportSRA SubmissionVariant CallingAssessment Toolbasespacelabs@illumina.comCompute cost: FreeLicense cost: n/abasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/abasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/abasespacelabs@illumina.comCompute Cost: 3 iCredits per node/hrLicense Cost: n/aDemo Data LinkFor Research Use Only. Not for use in diagnostic procedures.4

Click here to return to page 1Gene Expression and RegulationApp nameSequencing application(s)Key functionalityVendor Bisulfite sequencing Alignment Methylation callingIllumina, Inc. Custom reference supportIllumina, Inc.DRAGEN MethylationPipelineDemo Data LinkDemo Data Link Custom genome supportCompute cost: 5 iCredits per node/hrLicense cost: n/aExample compute cost:Targeted methylation138M reads, 2 x 150 bpAnalysis cost 7.50 iCredits/sampleWhole-genome1,532M reads, 2 x 150 bpAnalysis cost 16.1 iCredits/sampleCompute cost: 5 iCredits per node/hrLicense cost: n/aDRAGEN ReferenceBuilderDemo Data Link Whole-transcriptome geneexpression Gene fusion detection Alignment Fusion detection Gene expressionIllumina, Inc. DNA-Protein Interactions ChIPSeq Uses MACS for peakidentificatoin and HOMERfor motif discoveryBaseSpace Labs Methylation profiling Whole-genome sequencing Targeted sequencing Analyze WGBS andtargeted bisulfitesequencing dataBaseSpace Labs Small RNA sequencing miRNA profiling Alignment Differential expressionB&Gu @ University of TorinoDRAGEN RNA PipelineDemo Data LinkChIPSeqCompute cost: 5 iCredits per node/hrLicense cost: n/aExample compute cost:2.6M reads, 2 x 75 bpAnalysis cost 0.5 iCredits/samplebasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aDemo Data mpute cost: 3 iCredits per node/hrLicense cost: n/aDemo Data LinkmiRNAs AnalysisDemo Data LinkFor Research Use Only. Not for use in diagnostic ompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:5M reads, 1 x 50 bpAnalysis cost 0.78 iCredits/sample5

Click here to return to page 1Gene Expression and Regulation (continued)App nameSequencing application(s)Key functionalityVendor Targeted gene expression(AmpliSeq for Illumina) Alignment Gene counts Fusion detectionIllumina, Inc. Transcriptome mining Gene expression Illumina, Inc. Transcriptome mining Gene expression Assembly of noveltranscripts Differential expressionIllumina, Inc. Small RNA sequencing miRNA profiling Alignment Classification of miRNAs,isomiRs, and piRNAs Novel miRNA & pre-miRNAdiscovery Differential expression Batch processingIllumina, Inc.RNA AmpliconDemo Data LinkRNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data LinkAlignment (STAR or TopHat)Gene countsTranscripts countsAnnotationVariant callingFusion detectionNovel transcript assemblyBatch processingRNA-Seq DifferentialExpressionDemo Data LinkSmallRNASmall RNASequencingDemoData LinkFor Research Use Only. Not for use in diagnostic procedures.Compute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:2.56M reads, 2 x 150 bpAnalysis cost 1.50 iCredits/sample1.8 License cost: n/aExample compute cost:mRNA: 25M reads, 2 x 75 bpAnalysis cost 6.02 iCredits/sampletotalRNA: 50M reads, 2 x 75 bpAnalysis cost 12.04 iCredits/sampleCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:mRNA: 25M reads, 2 x 75 bpAnalysis cost 37.64 iCredits/sampletotalRNA: 50M reads, 2 x 75 bpAnalysis cost 75.3 iCredits/sampleCompute cost: 3 iCredits per node/hrLicense cost: n/a6

Click here to return to page 1Microbial Genomics and MetagenomicsApp nameSequencing application(s)Key functionalityVendor 16S rRNA microbialcommunities profiling Taxonomic classification ofmicrobial communities Batch processing Support for customdatabasesIllumina, Inc. E. coli serotypeidentification Serotype identificationGoSeqIt Targeted sequencing RNA-Seq Immunology Reconsts full-lengthadaptive immunerepertoires fromRep-Seq data AlignmentCenter for Algorithmic Biotech. Fungal rRNA microbialcommunities profiling Taxonomic classification ofmicrobial communitiesBaseSpace Labs Shotgun metagenomics Host DNA removal Taxonomic classificationBaseSpace Labs Phylogenetic analysisThe Huttenhower Lab16S MetagenomicsDemo Data LinkCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:Input: FASTA of E. coli readsAnalysis cost 1 iCredits/sampleE. coli SerotypingDemo Data LinkIgReCDemo Data LinkITS MetagenomicsDemo Data LinkKraken MetagenomicsDemo Data Link MetagenomicsMetaPhlAnDemo Data LinkFor Research Use Only. Not for use in diagnostic procedures.Compute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:100K reads, 2 x 300 bpAnalysis cost 1.28 iCredits/sampleyana-safonova.github.io/ig repertoire constructorigtools support@googlegroups.comCompute cost: 3 iCredits per node/hrLicense cost: n/abasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:2.1M reads, 2 x 150 bpAnalysis cost 2 iCredits/samplebasespacelabs@illumina.comCompute cost: 3 iCredits per node/hrLicense cost: n/aExample compute cost:4M reads, 2 x 300 bpAnalysis cost 1.16 iCredits/sample40M reads, 2 x 300 bpAnalysis cost 11.16 nCompute cost: 3 iCredits per node/hrLicense cost: n/a7