For Research Use Only Not for use in diagnostic procedures

Biomedical and Basic Research ndash Genetic Analysis

App name Sequencing application(s) Key functionality Vendor

Amplicon DSDemo Data Link

bull Targeted Resequencing (TruSight Tumor 26 Panel)

bull Alignmentbull Somatic Variant Callingbull Annotation

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 150 bp cost = 070 iCreditssample

BWA AlignerDemo Data Link

bull Whole Genome Sequencingbull Targeted Sequencing

bull Alignmentbull Custom reference genomebull Batch processing

BaseSpace Labs

basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 M reads 2 x 150 bp cost = 2810 iCreditssample

BWA EnrichmentDemo Data Link

bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Annotationbull Custom Manifest Filesbull Batch processing

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 30 M reads 2 x 75 bp cost = 528 iCreditssample

Cancer Variant CallerDemo Data Link

bull Whole-Genome Sequencingbull Targeted Resequencing

bull Variant Calling Samsung

basespaceqasamsungcom Compute Cost 3 iCredits per nodehr License Cost na

EDGC Annotator

bull Targeted Resequencing bull Variant Annotationbull Variant Analysis

EONE-DIAGNOMICS Genome Center

wwwedgccomedgcannotatorlang=en Compute Cost 3 iCredits per nodehr License Cost na

EnrichmentDemo Data Link

bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Somatic Variant Callingbull SVCNV Callingbull Annotationbull Custom Manifest Filesbull Batch processing

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Exome (200x mean coverage) 60 M reads 2 x 75 bp cost = 676 iCreditssample

BaseSpacereg Sequence Hub Apps Quick GuideCredits are the common currency in which BaseSpace Sequence Hub services are priced Learn more about iCredits and billing

For Research Use Only Not for use in diagnostic procedures

Biomedical and Basic Research ndash Genetic Analysis (continued)

App name Sequencing application(s) Key functionality Vendor

GeneTalk Variant Analyzer

bull Targeted Resequencing bull Variant Annotationbull Variant Analysis

GeneTalk

wwwgene-talkdeCompute Cost Free License Cost na

LoFreq Rare Variant CallerDemo Data Link

bull Targeted Resequencingbull Oncology

bull Variant Caller Genome Institute of Singapore

wwwgisappsorglofreqbscontacthtmCompute Cost 3 iCredits per nodehr License Cost - 1 iCredit per 10 GB of input file - 4 iCredits for 30ndash39 GB - 5 iCredits 40ndash49 GB - etc

Melanoma Profiler

bull Targeted Resequencingbull Oncology

bull Variant Analysisbull Tumor Normal

Biomatters Ltd

appsbiomatterscommelanoma-profilerwelcome Compute Cost Free

mtDNA Variant AnalyzerDemo Data Link

bull Targeted Resequencingbull mtDNA Profilingbull Forensics

bull Visualizatoinbull Variant Analysis

Illumina Inc

Compute Cost FreeLicense Cost na

mtDNA Variant ProcessorDemo Data Link

bull Targeted Resequencingbull mtDNA Profilingbull Forensics

bull mtDNA Variant Calling Illumina Inc

Compute Cost Free License Cost na

MutationForecaster

bull RNA-Seqbull Variant Analysis

bull Interpret and validate mutations that affect mRNA splicing and protein coding

Cytognomix Inc

basespacemutationforecastercomCompute Cost Free License Cost - 1 Day Subscription 75 iCredits - 7 Day Subscription 125 iCredits

MyFLqDemo Data Link

bull Forensics bull STR and SNP query University Ghent

forensicugentbeCompute Cost 3 iCredits per nodehrLicense Cost na

For Research Use Only Not for use in diagnostic procedures

Biomedical and Basic Research ndash Genetic Analysis (continued)

App name Sequencing application(s) Key functionality Vendor

Novoalign Generic DNA pipelineDemo Data Link

bull Resequencing bull Alignmentbull Variant Calling

Novocraft

wwwnovocraftcomproductsnovoalignCompute Cost 3 iCredits per nodehr

NuGEN Ovation Target EnrichmentDemo Data Link

bull Targeted Resequencing bull Demultiplexingbull Alignment

NuGEN Technologies Inc

wwwnugencomCompute Cost 3 iCredits per nodehrLicense Cost na

Phy-Mer

bull Mitochondrial Analysis bull Haplogroup Analysis MEEI Bioinformatics Center (MBC)

githubcomdanielnavarrogomezphy-merCompute Cost 3 iCredits per nodehrLicense Cost na

TruSeqreg AmpliconDemo Data Link

bull Targeted Resequencing bull Alignmentbull Small Variant Callingbull Somatic Variant Callingbull Annotationbull Custom Manifest Filesbull Batch processing

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Myeloid Panel (5000x mean coverage) 235 M reads 2 x 150 bp cost = 078 iCreditssample

TruSeq Long-Read AssemblyDemo Data Link

bull TruSeq Synthetic Long Reads

bull Assembly of synthetic long reads

bull Phasing Analysis

Illumina Inc

Compute Cost Free License Cost na

TruSeq Phasing AnalysisDemo Data Link

bull Genetic Analysisbull Haplotype Resolution

bull Phasing Analysis Illumina Inc

Compute Cost Free License Cost na

For Research Use Only Not for use in diagnostic procedures

Biomedical and Basic Research ndash Genetic Analysis (continued)

App name Sequencing application(s) Key functionality Vendor

TruSight Tumor 15Demo Data Link

bull Targeted Resequencing (TruSight Tumor 15 Panel)

bull Alignmentbull Variant Calling

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSight Tumor 15 Panel (5000x mean coverage) 733 K reads 2 x 150 bp cost = 035 iCreditssample

TruSight Tumor 170

bull Targeted Resequencing (TruSight Tumor 170 Panel)

bull Variant Callingbull SVCNV Callingbull RNA Fusion Calling

Illumina Inc

Compute Cost FreeLicense Cost na

Tumor NormalDemo Data Link

bull Whole Genome Sequencing bull Variant Callingbull SVCNV Callingbull Annotationbull Tumor Normal Analysis

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost Whole Genome (80x Tumor40x Normal mean coverage) 18 B reads 2 x 100 bp cost = 9288 iCreditspair of samples

Whole Genome SequencingDemo Data Link

bull Whole Genome Sequencing bull Alignmentbull Small Variant Callingbull SVCNV Callingbull Annotationbull Batch Processing

Illumina Inc

Compute Cost 3iCredits per nodehr License Cost naWhole Genome (30x mean coverage)300 M reads 2 x 150 bpcost = 9ndash12 iCreditssample depending on sample quality

CrossMapDemo Data Link

bull Data conversion bull Converts genome coordinates between different assemblies

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na

For Research Use Only Not for use in diagnostic procedures

Data Handling Data Quality Control (QC) and Data Visualization

App name Sequencing application(s) Key functionality Vendor

Elastic Genome Browser

bull Resequencing (human) bull Genome Browserbull Visualizatoins

Strand Life Sciences

wwwstrandlscomCompute Cost Free License Cost na

FASTA Upload

bull Data Import bull Import FASTA files BioBam Bioinformatics SL

wwwbiobamcombasespaceappsCompute Cost Free License Cost na

FASTQ Toolkit

bull FASTQ Manipulation bull Sub-samplingbull Adapter Trimmingbull Base Trimmingbull Quality Trimmingbull Read Filtering

BaseSpace Labs

basespacelabsilluminacom Compute Cost 3 iCredits per nodehrLicense Cost na

FASTQCDemo Data Link

bull Data QC bull Base QC Profile BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehrLicense Cost na

Genome Profiler

bull Resequencing (human) bull Genome Browserbull Visualizations

Biomatters Ltd

appsbiomatterscommelanoma-profilerwelcomeCompute Cost FreeLicense Cost na

Integrative Genomics Viewer

bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq

bull Genome Browserbull Visualizations

BaseSpace Labs

basespacelabsilluminacomCompute Cost Free License Cost na

SRA Import

bull Data Importbull General NGS

bull Imports NGS data from NCBI Sequence Read Archive to BaseSpace Sequence Hub using SRA accession number

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

SRA Submission

bull Data Exportbull General NGS

bull Submission of data to NCBI SRA

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

For Research Use Only Not for use in diagnostic procedures

Data Handling Data Quality Control (QC) and Data Visualization (continued)

App name Sequencing application(s) Key functionality Vendor

USC BigWig GeneratorDemo Data Link

bull Data Conversion bull Convert data to BigWig file format

Ramsingh Lab Keck-Hematology

githubcomRamsinghLabCompute Cost 3 iCredits per nodehr License Cost na

Variant Calling Assessment ToolDemo Data Link

bull Data QC bull Comparison of variant call sets

bull SNV and Indel statistics

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

Gene Expression and Regulation

App name Sequencing application(s) Key functionality Vendor

ChIPSeqDemo Data Link

bull DNA-Protein Interactionsbull ChIPSeq

bull Uses MACS for peak identificatoin and HOMER for motif discovery

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

Cufflinks Assembly amp DEDemo Data Link

bull Transcriptome Miningbull Gene Expressoin

bull Assembly of novel transcripts

bull Differential Expression

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 1125 iCreditssample total RNA 50 M reads 2 x 75 bp cost = 2349 iCreditssample

DESeq2Demo Data Link

bull Transcriptome Miningbull Gene Expression

bull Differential Expression BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 3764 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 7528 iCreditssample

For Research Use Only Not for use in diagnostic procedures

Gene Expression and Regulation (continued)

App name Sequencing application(s) Key functionality Vendor

Genomatix Pathway System (GePS)Demo Data Link

bull Transcriptomebull ChIP-Seqbull Methyl-Seqbull Oncology

bull Pathway Analysisbull Genomatix

Genomatix

wwwgenomatixdeCompute Cost Free License Cost 7 Day Subscription 70 iCredits

iPathwayGuide

bull Transcriptomebull Proteomics

bull Pathway Analysis Advaita Bio

wwwadvaitabiocomCompute Cost Free License Cost - Single Report 149 iCredits- Annual Subscription 1995 iCredits

MethylSeqMethylKit Demo Data Link

bull Methylation Profilingbull Whole Genome Sequencingbull Targeted Sequencing

bull Analyze WGBS and targeted bisulfite sequencing data

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

MethylSeq

bull Whole Genome Sequencingbull Targeted Resequencingbull ChIP-Seqbull RNA-Seq

bull Alignmentbull Methylation Callingbull Custom manifestsbull Custom Genomebull Batch Processing

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost TruSeq Methyl Capture 55 M reads 2 x 100 bp cost = 1953 iCreditssample

miRNAs AnalysisDemo Data Link

bull Small RNA sequencingbull miRNA Profiling

bull Alignmentbull Differential Expression

BampGu University of Torino

mirnasanalysisbasespaceappblogspotit Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 M reads 1 x 50 bp cost = 078 iCreditssample

NextBio Annotates RNA-SeqDemo Data Link

bull Transcriptomebull Gene Expression

bull Gene Annotation using BaseSpace Correlation Engine

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

NuGEN Ovation Fusion DetectionDemo Data Link

bull Targeted RNA-Seq bull Alignmentbull Fusion Detection

NuGEN Technologies Inc

wwwnugencomCompute Cost 3 iCredits per nodehr License Cost na

For Research Use Only Not for use in diagnostic procedures

Gene Expression and Regulation (continued)

App name Sequencing application(s) Key functionality Vendor

RNA ExpressDemo Data Link

bull Transcriptome Miningbull Gene Expression

bull Assembly of novel transcripts with STAR

bull Differential Expression with DESeq

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 228 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 455 iCreditssample

RNA-Seq AlignmentDemo Data LinkDemo Data LinkDemo Data Link

bull Transcriptome Miningbull Gene Expression

bull Alignment (STAR or TopHat)bull Gene Countsbull Transcripts Countsbull Annotationbull Variant Callingbull Fusion Detectinbull Novel Transcript Assemblybull Batch Processing

Illumina Inc

18 License Cost na Example Compute Cost mRNA 25 M reads 2 x 75 bp cost = 602 iCreditssample totalRNA 50 M reads 2 x 75 bp cost = 1204 iCreditssample

Small RNASequencing

Small RNADemo Data Link

bull Small RNA sequencingbull miRNA Profiling

bull Alignmentbull Classification of miRNAs

isomiRs and piRNAsbull Novel miRNA amp pre-miRNA

discoverybull Differential Expressionbull Batch processing

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na

SureCell RNA Single-CellDemo Data LinkDemo Data Link

bull Transcriptome Miningbull Gene Expression

bull Cell Countsbull Alignmentbull Gene Countsbull Cell Filteringbull Transcripts Countsbull Reporting

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost1000 cells 100 K readscell 100 M reads 1 x 75 bp cost = 815 iCreditssample

TruSeq Targeted RNADemo Data Link

bull Targeted Gene Expression bull Gene Expression Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na

For Research Use Only Not for use in diagnostic procedures

Microbial Genomics and Metagenomics

App name Sequencing application(s) Key functionality Vendor

16s Metagenomics

16S MetagenomicsDemo Data Link

bull 16S rRNA Microbial Communities Profiling

bull Taxonomic classification of microbial communities

bull Batch processing

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 128 iCreditssample

DeepChekreg-HBVDemo Data Link

bull Viral Typing - HBV - HCV - HIV

bull Viral Typingbull Drug Resistance

ABL SA

ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 40 iCredits

DeepChekreg-HCVDemo Data Link

bull Viral Typing - HBV - HCV - HIV

bull Viral Typingbull Drug Resistance

ABL SA

ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 45 iCredits

DeepChekreg-HIVDemo Data Link

bull Viral Typing - HBV - HCV - HIV

bull Viral Typingbull Drug Resistance

ABL SA

ablsacomdiagnostic-solutionsdeepchek-assaysCompute Cost Free License Cost 65 iCredits

GENIUS Metagenomics Know NowDemo Data Link

bull Metagenomics bull Bacterial ID CosmosID

wwwcosmosidcombasespace-landing Compute Cost 3 iCredits per nodehr License Cost na

IgReCDemo Data Link

bull Targeted Sequencingbull RNA-Seqbull Immunology

bull Reconsts full-length adaptive immune repertoires from Rep-Seq data

bull Alignment

Center for Algorithmic Biotech

yana-safonovagithubioig_repertoire_constructorigtools_supportgooglegroupscomCompute Cost 3 iCredits per nodehr License Cost na

Kraken MetagenomicsDemo Data Link

bull Shotgun Metagenomics bull Host DNA Removalbull Taxonomic Classification

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 4 M reads 2 x 300 bp cost = 116 iCreditssample40 M reads 2 x 300 bp cost = 1116 iCreditssample

For Research Use Only Not for use in diagnostic procedures

Microbial Genomics and Metagenomics (continued)

App name Sequencing application(s) Key functionality Vendor

MetaPhlAnDemo Data Link

bull Metagenomics bull Phylogenetic Analysis The Huttenhower Lab

huttenhowersphharvard edumetaphlanCompute Cost 3 iCredits per nodehr License Cost na

MiXCR Immune Repertoire AnalyzerDemo Data Link

bull Targeted Sequencingbull RNA-Seqbull Immunology

bull Alignmentbull Visualization

MILaboratory

milaboratorycomsupportmilaboratorycomCompute Cost 3 iCredits per nodehr License Cost na

PEDANTTM SequenceAnalyzerDemo Data Link

bull Microbial bull Bacterial Sequence Analysis

Biomax Informatics AG

httpwwwbiomaxcomproductpedant-pro-sequence-analysis-suiteCompute Cost FreeLicense Cost - 15 KB - 2 iCredits

Prokka Genome AnnotationDemo Data Link

bull Microbial bull Prokaryotic Genome Annotation

BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

QIIME PreprocessingDemo Data Link

bull Microbiome Analysis bull Taxonomic classification of microbial communities

bull Phylogenetic reconstructionbull Batch processing

QIIME Development Team

qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 004 iCreditssample

QIIME VisualizationsDemo Data Link

bull Microbiome Analysis bull Visualization QIIME Development Team

qiimeorgCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 100 K reads 2 x 300 bp cost = 071 iCreditssample

For Research Use Only Not for use in diagnostic procedures

Microbial Genomics and Metagenomics (continued)

App name Sequencing application(s) Key functionality Vendor

Rescaf

bull Microbial bull Improves quality of scaffold sequences

BaseSpace Labs

basespacelabsilluminacom Compute Cost 3 iCredits per nodehr License Cost na

SEAR Antibiotic ResistanceDemo Data Link

bull Metagenomicsbull Microbiome

bull Construct Antimicrobial Resistance Genes

University of Cambridge

githubcomwill-roweSEARCompute Cost 3 iCredits per nodehr License Cost na

SPAdes Genome AssemblerDemo Data Link

bull Microbial bull De novo Assembly Algorithmic Biology Lab

cabspburuspadesCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage 833 K reads 2 x 300 bp cost = 730 iCreditssample

SRST2Demo Data Link

Demo Data Link

bull Microbial ID bull MLST Typing BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

String Graph AssemblerDemo Data Link

bull Mid-size Genome Assembler

bull Assembly BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na

Velvet de novo AssemblyDemo Data Link

bull Microbial bull de novo Assembly BaseSpace Labs

basespacelabsilluminacomCompute Cost 3 iCredits per nodehr License Cost na Example Compute Cost 5 MB genome with 100x coverage833 K reads 2 x 300 bpcost = 153 iCreditssample

For Research Use Only Not for use in diagnostic procedures

Proteomics

App name Sequencing application(s) Key functionality Vendor

OpenSWATHDemo Data Link

bull Mass Specbull Proteomics

bull Protein Analysis Aebersold Group ETH Zurich

wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na

OpenSWATH Assay GeneratorDemo Data Link

bull Mass Specbull Proteomics

bull Protein Analysis Aebersold Group ETH Zurich

wwwopenswathorgCompute Cost 3 iCredits per nodehr License Cost na

Protein Expression AssemblerDemo Data Link

bull Mass Specbull Proteomics

bull Protein Analysis SCIEX

sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na

Protein Expression ExtractorDemo Data Link

bull Mass Specbull Proteomics

bull Protein Analysis SCIEX

sciexcomswathcloudsupportsciexcomCompute Cost 3 iCredits per nodehr License Cost na

Protein Expression WorkflowDemo Data Link

bull Mass Specbull Proteomics

bull Protein Analysis SCIEX

sciexcomswathcloudsupportsciexcomCompute Cost FreeLicense Cost na

RNA-Seq Translator

bull Proteomicsbull RNA-Seq

bull Uses de novo transcriptome assembly to generate protein sequences

Yale University

robkitchenyaleeduCompute Cost 3 iCredits per nodehr License Cost na

For Research Use Only Not for use in diagnostic procedures

copy 2017 Illumina Inc All rights reserved Pub No 970-2015-003

wwwilluminacom

Proteomics (continued)

App name Sequencing application(s) Key functionality Vendor

Small RNASequencing

SWATH to MRM BuilderDemo Data Link

bull Small RNA sequencingbull miRNA Profiling

bull Alignmentbull Classification of miRNAs

isomiRs and piRNAsbull Novel miRNA amp pre-miRNA

discoverybull Differential Expressionbull Batch processing

Illumina Inc

Compute Cost 3 iCredits per nodehr License Cost na

SWATHAtlas Ion Library Generator

bull Proteomics bull Protein Analysis Institute for Systems Biology

wwwswathatlasorgCompute Cost Free License Cost na

Quality

App name Sequencing application(s) Key functionality Vendor

PicardSpaceDemo Data Link

bull Data QC bull Calculates alignment metrics

BaseSpace Labs

basespacelabsilluminacomPrice Free for bam lt1 Compute Cost FreeCompute Cost Free MB 1 iCredit for bam gt 1 Compute Cost Free Compute Cost Free MB License Cost na