BaseSpace. Genomics cloud computing. Illumina


BaseSpace makes sample and run management easy with new Prep feature, which enables even closer integration between BaseSpace and the NextSeq sequencing platform. You can plan your entire workflow from sample creation to library prep, and pooling to sequencing. Once a run has been planned and is ready to sequence, simply go to the instrument and select your run. No additional setup is required at the instrument. While this functionality is currently available only on NextSeq instruments, it will soon be updated to function for HiSeq and MiSeq. For now, HiSeq and MiSeq instruments will continue to use Illumina sample sheets.


Instrument integration

BaseSpace is the first cloud platform to be directly integrated in to the industry’s leading sequencing platforms, with no cumbersome and time consuming data transfer steps. Simply select the option to use BaseSpace for storage and analysis when starting a sequencing run on a MiSeq, HiSeq or NextSeq instrument. The instrument seamlessly pushes data to BaseSpace for automatic analysis and storage, with the option of retaining data for local hosting. There is no need for a manual and time-consuming data-transfer step. The data is already up in the cloud, for you and your collaborators to access anywhere, anytime.

Real-Time QC

SAV (Sequencing Analysis Viewer)

To enhance the run management utility of BaseSpace we have now integrated the capabilities of “Sequence Analysis Viewer” (SAV) directly into the user interface, removing the need to install separate software but keeping the same charts and same look and feel as the current SAV. It allows for the real-time, cycle-by-cycle monitoring of the most useful primary metrics coming off the sequencing instruments. This data is updated real-time and can be used during and after your run.

Featured Apps


Assemble bacteria de novo - FREE


DNASTAR SeqMan NGen allows you to perform de novo assembly of bacterial genome sequences.


Align, assemble & analyze reads


DNASTAR software for comprehensive next-gen sequence assembly and analysis.


BWA Whole Genome Sequencing

Illumina, Inc.

BWA/GATK Alignment and Variant Calling


BWA Enrichment

Illumina, Inc

The core algorithms in the BWA Enrichment workflow are the BWA Genome Alignment Software and the GATK Variant Caller.


Genomatix Pathway System (GePS)


Generation and Visualization of pathways, networks and processes.


Elastic Genome Browser

Strand Life Sciences

Expand and compress multiple genomic regions to verify large SVs, fusion genes, and novel splice junctions with Strand's eGB.


HiSeq Isaac Human WGS Workflow

Illumina Inc.

Isaac Genome Alignment Software and Isaac Variant Caller


Genome Profiler

Biomatters Ltd

Beautifully rendered, remotely managed, securely delivered polyomic analysis. Starting with the best Genome Browser in the cloud


Isaac Whole Genome Sequencing v2

Illumina, Inc.

Isaac Whole Genome Alignment Software and Variant Calling


Isaac Enrichment

Illumina, Inc

The core algorithms in the Isaac Enrichment workflow are the Isaac Genome Alignment Software and the Isaac Variant Caller.


Omixon HLA Typing

Omixon Biocomputing

HLA typing based on targeted sequencing, exome data or whole genome.


Melanoma Profiler

Biomatters Ltd

Analyze your melanoma samples automatically. Visualize the results in a dynamic, intuitive viewer.


PathSEQ Virome

PathGEN Dx Pte Ltd

Virus detection in sequencing data




OncoMD is a tool that provides information about cancer related mutations, curated from published research.


The Broad's IGV

Broad Institute

Integrative Genomics Viewer (IGV)




PicardSpace calculates alignment metrics with the open-source tool Picard.


Variant Interpreter


Provides a summary report for clinical and biological insights relevant to disease-specific genomic alterations in a tumor.


Tumor Normal

Illumina, Inc.

Isaac Whole Genome Alignment Software and Strelka Variant Caller

Illumina Workflows


Custom/PCR Amplicon


The Custom/PCR Amplicon workflow evaluates short regions of amplified DNA (amplicons) for variants.


De Novo Assembly


The Assembly workflow enables de novo assembly of a reference genome directly from the sequencing reads.


Library QC


The Library QC workflow is intended for evaluating the abundance, fragment length, and sample quality of DNA libraries.


Metagenomics Analysis


The Metagenomics workflow enables the analysis of 16S ribosomal RNA, a component of the 30S subunit of prokaryotic ribosomes.




The Resequencing workflow compares the DNA sequence in the sample(s) against a reference genome and identifies any variants (SNPs or indels) relative to the reference sequence.


Small RNA Analysis


The Small RNA workflow measures the abundance of various types of short RNA sequences, particularly miRNA. It is suitable for identifying and quantifying miRNA expression and for comparing abundance across samples.