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

 

Amplicon DS

Illumina, Inc.

Enables streamlined analysis of the Illumina TruSight Tumor Panel.

 

16S Metagenomics

Illumina, Inc.

Analyzes DNA from amplicon sequencing of prokaryotic 16S small subunit rRNA genes. Provides visuals of taxonomic classification.

 

BWA Enrichment

Illumina, Inc.

Performs targeted resequencing using BWA, the community’s most popular algorithm for alignment, and GATK for variant calling.

 

BWA Enrichment

Illumina, Inc.

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

 

BWA Whole Genome Sequencing v1.0

Illumina, Inc.

Processes whole-genome sequencing data using BWA alignment and GATK variant calling.

 

BWA Enrichment v1.0

Illumina, Inc.

Performs targeted resequencing using BWA, the community’s most popular algorithm for alignment, and GATK for variant calling.

 

Cufflinks Assembly & DE

Illumina, Inc.

Quickly assesses novel transcript isoforms and gene expression levels. Seamlessly integrated with the TopHat Alignment App.

 

ChIPSeq

BaseSpace Labs

Identifies transcription factor binding sites using MACS2, and discovers motifs within the peaks using HOMER.

 

DeepChek®-HCV

ABL S.A.

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

 

DeepChek®-HBV

ABL S.A.

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

 

EDGC Annotator

EONE-DIAGNOMICS Genome Center

EDGC Annotator is an efficient app that annotates functionally genetic variants from human genome by providing information.

 

DeepChek®-HIV

ABL S.A.

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

 

FASTA Upload

BioBam Bioinformatics S.L.

Upload nucleotide or peptide sequences in FASTA format to your BaseSpace projects.

 

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.

 

FASTQ Toolkit

BaseSpace Labs

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

 

FASTQ Toolkit

BaseSpace Labs

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

 

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.

 

GENIUS Metagenomics: Know Now

CosmosID

Rapid and actionable bacterial identification to the species, subspecies and strain level based on our curated database.

 

GENIUS Metagenomics: Know Now

CosmosID

Rapid and actionable bacterial identification to the species, subspecies and strain level based on our curated database.

 

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.

HiSeq Isaac Human Whole Genome Sequencing Workflow uses Isaac core algorithms for genome alignment and variant calling.

 

Isaac Enrichment

Illumina, Inc.

Performs targeted resequencing using fast and accurate Isaac algorithms for alignment and variant calling.

 

Isaac Enrichment

Illumina, Inc.

Performs human whole-genome phasing for analysis of alleles originating from separate chromosomes.

 

Isaac Whole Genome Sequencing

Illumina, Inc.

Quickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.

 

Isaac Enrichment v1.0

Illumina, Inc.

Performs targeted resequencing using fast and accurate Isaac algorithms for alignment and variant calling.

 

Kraken Metagenomics

BaseSpace Labs

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

 

Isaac Whole Genome Sequencing v2

Illumina, Inc.

Quickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.

 

Melanoma Profiler

Biomatters Ltd

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

 

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.

 

MethylKit

BaseSpace Labs

MethylKit analyzes and annotates DNA methylation from high-throughput bisulfite sequencing data.

 

MetaPhlAn

Huttenhower Lab, HSPH

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

 

MethylSeq

Illumina, Inc.

DNA methylation analysis for epigenetic studies. Analyzes DNA that has been sequenced using the TruSeq DNA Methylation Kit.

 

MethylKit

BaseSpace Labs

MethylKit analyzes and annotates DNA methylation from high-throughput bisulfite sequencing data.

 

MiXCR Immune Repertoire Analyzer

MiLaboratory

T- and B- cell receptor repertoire sequencing data analysis: V-(D)-J segment mapping and clonotype assembly

 

miRNAs Analysis

B&Gu @ University of Torino

This app allows the detection of differentially expressed miRNAs between two conditions. Results are saved in data folder.

 

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

MedGenome

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

 

Phy-Mer v1.0b

MEEI Bioinformatics Center (MBC)

A novel aligment-free and reference-independent mitochondrial haplogroup classifier

 

PEDANT SequenceAnalyzer

Biomax Informatics AG

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

 

Prokka Genome Annotation

BaseSpace Labs

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

 

PicardSpace

BaseSpace Labs

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

 

Protein Expression Extractor

SCIEX

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

 

Protein Expression Assembler

SCIEX

Analysis of differential protein expression.

 

RNA Express

Illumina, Inc.

Performs RNA-Seq read alignment and differential gene expression in a convenient and rapid analysis package.

 

Protein Expression Workflow

SCIEX

Analytics and visualization tools for results produced by Protein Expression Extractor and Protein Expression Assembler.

 

Small RNA

Illumina, Inc.

Aligns reads and outputs hits. Performs optional novel precursor discovery and pairwise differential expression analysis

 

RNA-Seq Translator

Yale University

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

 

SPAdes Genome Assembler

Algorithmic Biology Lab

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

 

SPAdes Genome Assembler

Algorithmic Biology Lab

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

 

SRA Submission

BaseSpace Labs

This app assists in sending your data from BaseSpace to NCBI's Sequence Read Archive (SRA).

 

SRA Import

BaseSpace Labs

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

 

String Graph Assembler

BaseSpace Labs

App performs a contig assembly, builds scaffolds, removes mate pair adapter sequences, and calculates assembly quality metrics.

 

SRST2

BaseSpace Labs

For bacteria. Reports sequence types from multi locus sequence typing database and reference genes from gene sequence database.

 

The Broad's IGV

Broad Institute

Integrative Genomics Viewer (IGV)

 

SWATHAtlas Ion Library Generator

Institute for Systems Biology

App to facilitate creation of custom SWATH Ion Libraries

 

TruSeq Amplicon

Illumina, Inc.

Streamlined analysis of NGS data enriched for particular target sequences using TruSeq Amplicon reads.

 

TopHat Alignment

Illumina, Inc.

Aligns RNA reads and detects gene fusions using the industry-standard method. Integrated with the Cufflinks Assembly & DE App.

 

TruSeq Phasing Analysis

Illumina, Inc.

Performs human whole-genome phasing for analysis of alleles originating from separate chromosomes.

 

TruSeq Long-Read Assembly

Illumina, Inc.

Constructs synthetic long reads from shorter sequencing reads, for genome assembly, genome finishing, and de novo assembly.

 

Tumor Normal

Illumina, Inc.

Detects somatic variants from a tumor and matched normal sample pair; algorithms for whole-genome alignment and variant calling.

 

TruSeq Targeted RNA

Illumina, Inc.

Analyzes RNA samples prepared using TruSeq Targeted RNA Expression Kits. Aligns reads, quantifies relative expression

 

Variant Calling Assessment Tool

BaseSpace Labs

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

 

USC BedGraph Converter

Ramsingh Lab Keck-Hematology

This application is used to convert the bigwig files output from other apps which produce bedgraph files for IGV.

 

Variant Calling Assessment Tool

BaseSpace Labs

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

 

Variant Calling Assessment Tool

BaseSpace Labs

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

 

VariantStudio App

Illumina, Inc.

Tool leverages leading annotation databases and a powerful filtering interface to rapidly identify disease-associated variants.

 

Variant Interpreter

N-of-One

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

 

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.