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.
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Click on any of the application areas below to quickly view each section.
Biomedical and Basic Research – Genetic Analysis	���������������������������������������������������������������������������������Pages 1–3
Data Handling, Data Quality Control (QC), and Data Visualization.  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  Page 4
Gene Expression and Regulation .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  . Pages 5–6
Microbial Genomics and Metagenomics.  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .Pages 7–8

Biomedical and Basic Research – Genetic Analysis
App nameSequencing application(s)Key functionalityVendor• Whole-exome sequencing• Targeted Resequencing• Alignment• Small Variant Calling• Somatic Variant Calling• SV/CNV Calling• Custom Manifest Files

Illumina, Inc.

• Whole-genome sequencing• Whole-exome sequencing• Alignment• Small variant calling• CNV calling• Somatic variant calling

Illumina, Inc.

• De novo variant calling• Novel variant identification

Illumina, Inc.

DRAGEN Enrichment
Demo Data Link

DRAGEN Germline
Demo Data Link

DRAGEN Joint
Genotyping Pipeline
Demo Data Link

For Research Use Only. Not for use in diagnostic procedures.

Compute Cost: 2 iCredits per node/hr
License Cost: n/a
Example Compute Cost:
FASTQ to SNVs only
88M reads, 2 x 150 bp
Analysis cost = 2.50 iCredits/sample

Compute cost: 7 iCredits per node/hr
License cost: n/a
Example compute cost:
FASTQ to SNVs only
88M reads, 2 x 150 bp
Analysis cost = 2.50 iCredits/sample

Compute cost: 5 iCredits per node/hrLicense cost: n/aExample compute cost:
Input: Trio of gVCFs processed with
DRAGEN Germline
Analysis cost = 1 iCredits/sample

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Biomedical and Basic Research – Genetic Analysis (continued)
App nameSequencing application(s)Key functionality

Vendor• Whole-genome sequencing• Whole-exome sequencing• Alignment• Somatic variant calling• Tumor-normal andtumor-only analysis

Illumina, Inc.

• Whole-genome sequencing• Targeted sequencing• Alignment• Custom reference genome• Batch processing

BaseSpace Labs

• Targeted resequencing(AmpliSeq™ for Illumina)• Alignment• Small variant calling• Annotation

Illumina, Inc.

• Targeted Resequencing• Variant Annotation• Variant Analysis

EONE-DIAGNOMICS Genome Center• Targeted resequencing(AmpliSeq™ for Illumina)• CNV calling

BaseSpace Labs

• Targeted resequencing(AmpliSeq™ for Illumina)• CNV calling

DRAGEN SomaticPipeline
Demo Data Link

BWA Aligner
Demo Data Link

DNA Amplicon
Demo Data Link 1
Demo Data Link 2

EDGC Annotator

Demo Data Link

Demo Data Link

For Research Use Only. Not for use in diagnostic procedures.

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
0.72M reads, 2 x 150 bp
Analysis cost = 2 iCredits/sample

Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:-0.72M reads, 2 x 150 bp
Analysis cost = 2 iCredits/sample

www.edgc.com/edgcannotator?lang=en
Compute Cost: 3 iCredits per node/hr
License Cost: n/abasespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
18M reads, 2 x 150 bp
Analysis cost = 1 iCredits/sample

OncoCNV Trainer

OncoCNV Caller

Compute cost: 5 iCredits per node/hr
License cost: n/a
Example compute cost:
4,750M reads, 2 x 150 bp
Analysis cost = 13 iCredits/sample

BaseSpace Labs
basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
18M reads, 2 x 150 bp
Analysis cost = 1.5 iCredits/sample

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Biomedical and Basic Research – Genetic Analysis (continued)
App nameSequencing application(s)Key functionalityVendor• Targeted resequencing(AmpliSeq™ for Illumina)• Insertion and deletion
breakpoint detection

BaseSpace Labs

• Targeted resequencing• Low-frequency somaticvariant detection

BaseSpace Labs

• Alignment• Small variant calling• Somatic variant calling• Annotation• Custom manifest files• Batch processing

Illumina, Inc.

• Targeted resequencing(TruSight Tumor 15 Panel)• Alignment• Variant calling

Illumina, Inc.

• Targeted resequencing(TruSight Tumor 170 Panel)• Variant calling• SV/CNV calling• RNA fusion calling

Illumina, Inc.

• Targeted resequencing(TruSight® Tumor 170)

• Reduce PCR orsequencing errors forrare and low-frequency
somatic variants

BaseSpace Labs

PindelDemo Data Link

Pisces Variant Caller
Demo Data Link

• Targeted resequencing

TruSeq® Amplicon
Demo Data Link

TruSight Tumor 15
Demo Data Link

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
4.1M reads, 2 x 150 bp
Analysis cost = 1 iCredits/sample

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
7M reads, 2 x 150 bp
Analysis cost = 3 iCredits/sample

Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
TruSight Myeloid Panel(5000x mean coverage)
2.35M reads, 2 x 150 bp
Analysis cost = 0.78 iCredits/sample

Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
TruSight Tumor 15 Panel(5000x mean coverage)
733K reads, 2 x 150 bp
Analysis cost = 0.35 iCredits/sample

Compute cost: Free
License cost: n/a

TruSight Tumor 170

UMI Error Correction
Demo Data Link
Demo Data Link

For Research Use Only. Not for use in diagnostic procedures.

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
83M reads, 2 x 125 bp
Analysis cost = 2.15 iCredits/sample

3

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Data Handling, Data Quality Control (QC), and Data Visualization
App nameSequencing application(s)Key functionality

Vendor• FASTQ manipulation• Sub-sampling• Adapter trimming• Base trimming• Quality trimming• Read filtering

BaseSpace Labs

• Base QC profile

BaseSpace Labs

FASTQ Toolkit• Data QC

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/abasespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a

FASTQC
Demo Data Link

Integrative Genomics
Viewer• Whole-genome sequencing• Targeted resequencing• ChIP-Seq• RNA-Seq• Genome browser• Visualizations

BaseSpace Labs

• Data import• General NGS• Imports NGS data fromNCBI Sequence Read
Archive to BaseSpace
Sequence Hub using SRA
accession number

BaseSpace Labs

• Data export• General NGS• Submission of data to
NCBI SRABaseSpace Labs

• Data QC• Comparison of variant
call sets• SNV and Indel statistics

BaseSpace LabsSRA ImportSRA Submission

Variant Calling
Assessment Toolbasespacelabs@illumina.com
Compute cost: Free
License cost: n/abasespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/abasespacelabs@illumina.com
Compute cost: 3 iCredits per node/hrLicense cost: n/abasespacelabs@illumina.com
Compute Cost: 3 iCredits per node/hr
License Cost: n/a

Demo Data Link

For Research Use Only. Not for use in diagnostic procedures.

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Gene Expression and Regulation
App nameSequencing application(s)Key functionalityVendor• Bisulfite sequencing• Alignment• Methylation calling

Illumina, Inc.

• Custom reference support

Illumina, Inc.

DRAGEN Methylation
Pipeline
Demo Data Link
Demo Data Link

• Custom genome support

Compute cost: 5 iCredits per node/hr
License cost: n/aExample compute cost:
Targeted methylation
138M reads, 2 x 150 bp
Analysis cost = 7.50 iCredits/sample
Whole-genome
1,532M reads, 2 x 150 bp
Analysis cost = 16.1 iCredits/sample

Compute cost: 5 iCredits per node/hr
License cost: n/a
DRAGEN Reference
Builder
Demo Data Link

• Whole-transcriptome geneexpression• Gene fusion detection• Alignment• Fusion detection• Gene expression

Illumina, Inc.

• DNA-Protein Interactions• ChIPSeq• Uses MACS for peakidentificatoin and HOMER
for motif discovery

BaseSpace Labs

• Methylation profiling• Whole-genome sequencing• Targeted sequencing• Analyze WGBS andtargeted bisulfite
sequencing data

BaseSpace Labs

• Small RNA sequencing• miRNA profiling• Alignment• Differential expression

B&Gu @ University of Torino

DRAGEN RNA Pipeline
Demo Data Link

ChIPSeq

Compute cost: 5 iCredits per node/hr
License cost: n/a
Example compute cost:
2.6M reads, 2 x 75 bp
Analysis cost = 0.5 iCredits/sample

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a

Demo Data Link

MethylKit
MethylSeq

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a

Demo Data Link

miRNAs Analysis
Demo Data Link

For Research Use Only. Not for use in diagnostic procedures.

mirnasanalysisbasespaceapp.blogspot.it
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
5M reads, 1 x 50 bp
Analysis cost = 0.78 iCredits/sample

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Gene Expression and Regulation (continued)
App nameSequencing application(s)Key functionality

Vendor• Targeted gene expression(AmpliSeq™ for Illumina)• Alignment• Gene counts• Fusion detection

Illumina, Inc.

• Transcriptome mining• Gene expression• Alignment (STAR or TopHat)• Gene counts• Transcripts counts• Annotation• Variant calling• Fusion detection• Novel transcript assembly• Batch processing

Illumina, Inc.

• Transcriptome mining• Gene expression• Assembly of noveltranscripts• Differential expression

Illumina, Inc.

• Small RNA sequencing• miRNA profiling• Alignment• Classification of miRNAs,
isomiRs, and piRNAs• Novel miRNA & pre-miRNAdiscovery• Differential expression• Batch processing

Illumina, Inc.

RNA Amplicon
Demo Data Link

RNA-Seq AlignmentDemo Data Link
Demo Data Link
Demo Data Link

RNA-Seq Differential
Expression
Demo Data Link

SmallRNA
Small RNA

Sequencing
DemoData Link

For Research Use Only. Not for use in diagnostic procedures.

Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
2.56M reads, 2 x 150 bp
Analysis cost = 1.50 iCredits/sample

1.8 License cost: n/a
Example compute cost:
mRNA: 25M reads, 2 x 75 bp
Analysis cost = 6.02 iCredits/sample
totalRNA: 50M reads, 2 x 75 bp
Analysis cost = 12.04 iCredits/sample

Compute cost: 3 iCredits per node/hr
License cost: n/aExample compute cost:
mRNA: 25M reads, 2 x 75 bp
Analysis cost = 37.64 iCredits/sample
totalRNA: 50M reads, 2 x 75 bp
Analysis cost = 75.3 iCredits/sample

Compute cost: 3 iCredits per node/hr
License cost: n/a6

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Microbial Genomics and Metagenomics
App nameSequencing application(s)Key functionality

Vendor• 16S rRNA microbialcommunities profiling• Taxonomic classification ofmicrobial communities• Batch processing• Support for custom
databases

Illumina, Inc.

• E. coli serotypeidentification• Serotype identification

GoSeqIt• Targeted sequencing• RNA-Seq• Immunology• Reconsts full-length
adaptive immune
repertoires fromRep-Seq data
• Alignment

Center for Algorithmic Biotech.

• Fungal rRNA microbialcommunities profiling• Taxonomic classification of
microbial communities

BaseSpace Labs

• Shotgun metagenomics• Host DNA removal• Taxonomic classification

BaseSpace Labs

• Phylogenetic analysis

The Huttenhower Lab

16S Metagenomics
Demo Data Link

Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
Input: FASTA of E. coli reads
Analysis cost = 1 iCredits/sample

E. coli Serotyping
Demo Data Link

IgReC
Demo Data Link

ITS Metagenomics
Demo Data Link

Kraken Metagenomics
Demo Data Link

• Metagenomics

MetaPhlAn
Demo Data Link

For Research Use Only. Not for use in diagnostic procedures.

Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
100K reads, 2 x 300 bp
Analysis cost = 1.28 iCredits/sample

yana-safonova.github.io/ig_repertoire_constructor
igtools_support@googlegroups.com
Compute cost: 3 iCredits per node/hr
License cost: n/abasespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
2.1M reads, 2 x 150 bp
Analysis cost = 2 iCredits/sample

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
4M reads, 2 x 300 bp
Analysis cost = 1.16 iCredits/sample
40M reads, 2 x 300 bp
Analysis cost = 11.16 iCredits/sample

huttenhower.sph.harvard
edu/metaphlan
Compute cost: 3 iCredits per node/hr
License cost: n/a7

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Microbial Genomics and Metagenomics (continued)
App nameSequencing application(s)Key functionalityVendor• Targeted requencing• RNA-Seq• Immunology• Alignment• Visualization

MILaboratory• Microbial• Prokaryotic genome
annotation

BaseSpace Labs

• Improves quality of scaffold
sequences

BaseSpace Labs

• De novo assembly

Algorithmic Biology Lab

MiXCR Immune
Repertoire Analyzer

milaboratory.com
support@milaboratory.com
Compute cost: 3 iCredits per node/hr
License cost: 10 iCredits/sample

Demo Data Link

Prokka GenomeAnnotation

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a

Demo Data Link

• Microbial

Rescaf• Microbial

basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a

cab.spbu.ru/spades
Compute cost: 3 iCredits per node/hr
License cost: n/a
Example compute cost:
5MB genome with 100x coverage
833K reads, 2 x 300 bp
Analysis cost = 7.30 iCredits/sample

SPAdes Genome
Assembler
Demo Data Link

• Microbial ID

SRST2Demo Data Link
Demo Data Link

www.illumina.com
For Research Use Only. Not for use in diagnostic procedures.
© 2020 Illumina, Inc. All rights reserved. Pub. No. 970-2015-003 QB 8360

• MLST typing

BaseSpace Labs
basespacelabs@illumina.com
Compute cost: 3 iCredits per node/hr
License cost: n/a