BaseSpace. Genomics cloud computing. Illumina

Prep

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.

Sequence

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

 

Align, assemble & analyze reads

DNASTAR, Inc.

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

 

16S Metagenomics v1.0

Illumina, Inc.

The 16S Metagenomics app performs taxonomic classification of 16S rRNA targeted amplicon reads using the GreenGenes database.

 

Assemble bacteria de novo - FREE

DNASTAR, Inc.

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

 

Amplicon DS v1.1

Illumina, Inc.

Amplicon Dual Strand Panel Analysis Application

 

BWA Enrichment v2.0

Illumina, Inc.

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

 

BWA Enrichment v1.0

Illumina, Inc.

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

 

BWA Whole Genome Sequencing v1.0

Illumina, Inc.

BWA/GATK Alignment and Variant Calling

 

BWA Enrichment v2.1

Illumina, Inc.

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

 

DeepChek®-HBV v1.3

ABL S.A.

DeepChek®-HBV performs HBV deep sequencing analyses and reports on subtyping, genotyping and inferred levels of resistance

 

Cufflinks Assembly & DE

Illumina, Inc.

Perform novel transcript assembly and differential expression analysis on RNA samples with Cufflinks 2.1.1

 

DeepChek®-HIV

ABL S.A.

DeepChek®-HIV performs HIV deep sequencing analyses and reports on subtyping, genotyping and inferred levels of resistance

 

DeepChek®-HCV v1.3

ABL S.A.

DeepChek®-HCV performs HCV deep sequencing analyses and reports on subtyping, genotyping and inferred levels of resistance

 

FASTQ Toolkit v1.0

BaseSpace Labs

Allows manipulation of FASTQ files, including adapter trimming, quality trimming, length filtering, and down-sampling.

 

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.

 

GeneTalk Variant Analyzer

GeneTalk GmbH, Berlin

Easily analyze, filter, and annotate your VCF files.

 

FastQC

BaseSpace Labs

FastQC is used to quality control checks on raw sequence data coming from high throughput sequencing pipelines.

 

Genome Profiler

Biomatters Ltd

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

 

Genomatix Pathway System (GePS)

Genomatix

Generation and Visualization of pathways, networks and processes.

 

iPathwayGuide

Advaita Bio

Next-Gen Pathway Analysis for gene and protein expression

 

HiSeq Isaac Human WGS Workflow

Illumina, Inc.

Isaac Genome Alignment Software and Isaac Variant Caller

 

Isaac Enrichment v2.0

Illumina, Inc.

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

 

Isaac Enrichment v1.0

Illumina, Inc.

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

 

Isaac Whole Genome Sequencing v2

Illumina, Inc.

Isaac Whole Genome Alignment Software and Variant Calling

 

Isaac Enrichment v2.1

Illumina, Inc.

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

 

LoFreq Rare Variant Caller

Genome Institute of Singapore

LoFreq is a fast and sensitive variant-caller for inferring single-nucleotide variants from high-throughput sequencing data.

 

Kraken Metagenomics

BaseSpace Labs

Kraken Metagenomics assigns taxonomic labels to short DNA sequences with high sensitivity and speed.

 

MetaPhlAn

Huttenhower Lab, HSPH

The Metagenomic Phylogenetic Analysis tool profiles microbial community composition from metagenomic shotgun sequencing data.

 

Melanoma Profiler

Biomatters Ltd

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

 

NextBio Annotates RNA-Seq

BaseSpace Labs

Differentially expressed genes from RNA-seq are annotated with curated data from NextBio Research.

 

MyFLq

University Ghent

My F(orensic) L(oci) q(ueries) Open source, straightforward analysis tool for forensic DNA samples and profile generation.

 

Novoalign Generic DNA pipeline

Novocraft

Novoalign is an alignment tool for Illumina reads and accurately maps reads to a reference genome.

 

NextBio Transporter

BaseSpace Labs

Run this app after Cufflinks or RNA Express to send your results to NextBio Research.

 

PathSEQ Virome

PathGEN Dx Pte Ltd

Virus detection in sequencing data

 

OncoMD

SciGenom

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

 

PicardSpace

Illumina, Inc.

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

 

PEDANT SequenceAnalyzer

Biomax Informatics AG

The PEDANT™ BaseSpace App offers a specialized analysis workflow for bacterial DNA sequences.

 

Protein Expression Analytics

AB SCIEX

Analytics tools for results produced by the Protein Expression Assembler application.

 

Prokka Genome Annotation

BaseSpace Labs

Rapidly annotate genes and identify coding regions in prokaryotic genomes, from de novo assembly sequences.

 

Protein Expression Browser

AB SCIEX

Visualization of the results produced by the Protein Expression Assembler application.

 

Protein Expression Assembler

AB SCIEX

Analysis of differential protein expression.

 

RNA Express v1.0

Illumina, Inc.

Align RNA reads with the STAR aligner, followed by differential expression with DESeq2

 

Protein Expression Extractor

AB SCIEX

Quantitative analysis of protein expression in sample data acquired using the AB SCIEX SWATH™ method.

 

SPAdes Genome Assembler 3.0

Algorithmic Biology Lab

De Novo assembler suitable for single-cell and isolate genomes.

 

RNA-Seq Translator v1.0

Yale University

Performs a 3-frame translation of the differentially expressed genes from the Cufflinks App and generates a protein fasta file

 

SWATHAtlas Ion Library Generator

Institute for Systems Biology

App to facilitate creation of custom SWATH Ion Libraries

 

SRA Import

BaseSpace Labs

Tool to import Illumina data from NCBI's Sequence Read Archive into BaseSpace.

 

TopHat Alignment

Illumina, Inc.

Perform spliced alignment, variant calling, and reference quantification for RNA samples.

 

The Broad's IGV

Broad Institute

Integrative Genomics Viewer (IGV)

 

TruSeq Long-Read Assembly v1.1

Illumina, Inc.

This app assembles synthetic long-reads using data generated from the accompanying TruSeq Synthetic Long-Read Library Prep Kit.

 

TruSeq Amplicon v1.1

Illumina, Inc.

TruSeq Amplicon panel analysis application

 

Tumor Normal v1.1

Illumina, Inc.

Isaac Whole Genome Alignment Software and Strelka Variant Caller

 

TruSeq Phasing Analysis v1.1

Illumina, Inc.

This app performs human genome phasing using reads from the accompanying TruSeq Synthetic Long-Read Library Prep Kit.

 

Variant Interpreter

N-of-One

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

 

Tute Genomics

Tute Genomics

Annotate and prioritize genetic variants and genes in genome, exome, or gene panel sequencing experiments in a matter of minutes

 

VCAT v2.0

BaseSpace Labs

The Variant Calling Assessment Tool enables the comparison of variant call sets using VCF files as input.

 

VariantStudio App

Illumina, Inc.

Illumina VariantStudio App enables identification and biological interpretation of disease relevant variants.

 

Velvet de novo Assembly

BaseSpace Labs

De-novo assembly of bacteria using the Velvet assembler with a focus on Nextera Mate Pair data.

Illumina Workflows

 

Custom/PCR Amplicon

Illumina

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

 

De Novo Assembly

Illumina

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

 

Library QC

Illumina

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

 

Metagenomics Analysis

Illumina

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

 

Resequencing

Illumina

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

Illumina

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.