offers many different tools including alignment, RNA-Seq, DNA-Seq, ChIP-Seq, Small RNA-Seq, Genome Browser, visualizations, Biological Interpretation, etc. Supports workflows “one can import the sample data in FASTA, FASTQ or tag-count format. In addition, prealigned data in SAM, BAM or Illumina-specific ELAND format can be directly imported for analysis.”
Alignment feature: Supports alignment from Illumina, Ion Torrent, 454 (Roche), and Pac Bio
DNA-Seq Feature, can annotate with dbSNP

[CLC Genomics Workbench] (http://www.clcbio.com/desktop-applications/top-features/)

(QIAGEN). Features include: resequencing, workflow, read mapping, de novo assembly, variant detection, RNA-Seq, ChIP-Seq, Genome Browser, etc (entire list on website); Main Workbench offers database search (Genbank, Blast, Pubmed); 2000 organizations have invested in CLC
Accepts VCF files from 1000 Genomes Project
Accepts downloaded tracks from dbSNP
Also accepts: FASTA, GFF/GTF/GVF, BED, Wiggle, Cosmic, UCSC variant database, complete genomics master var file
Read mapping: “In addition to Sanger sequence data, reads from these high-throughput sequencing machines are supported: The 454 FLX System and the 454 GS Junior System from Roche, Illumina Genome Analyzer, Illumina HiSeq, Illumina HiScan, and Illumina MiSeq sequencing systems, SOLiD system from Life Technologies, Ion Torrent system from Life Technologies, Helicos from Helicos BioSciences”
De novo assembly: “In addition to Sanger sequence data, reads from these high-throughput sequencing machines are supported The 454 FLX System and the 454 GS Junior System from Roche, Illumina Genome Analyzer, Illumina HiSeq, Illumina HiScan, and Illumina MiSeq sequencing systems, SOLiD system from Life Technologies, Ion Torrent system from Life Technologies”
Annotation tracks from Ensembl

Private cloud repository -- formerly a redistributor of SRA and other NCBI resources; command-line or via web, can fetch data from a URL, build custom pipeline/ workflow has sra.dnanexus.com site: data downloads come directly from NCBI

[Ingenuity Variant Analysis] (http://www.ingenuity.com/products/variant-analysis)

(QIAGEN) allows for variant identification and analysis, uses NCI-60 data set for cancer, Supported third part informatin: Entrez Gene, RefSeq, ClinVar; gives contextual details of results instead of just A to B relationship
Has own database-- “knowledge base” based on COSMIC, OMIM, and TCGA databases

[Lasergene Genomics Suite] (http://www.dnastar.com/t-products-dnastar-lasergene-genomics.aspx)

Comprehensive NGS software pipeline for assembly, alignment, variant calling and analysis of NGS data
Supported workflows include: reference-guided and de novo genome and transcriptome assembly and analysis, metagenomics sample assembly, targeted resequencing, exome alignment, gene panels with validation control, variant analysis, and RNA-Seq, ChIP-Seq and miRNA alignment and analysis.
#1 in accuracy: fewer false negatives and better sensitivity compared to results obtained from other aligners
Aligns exome data and performs variant calling an average of 3 times faster than alternative pipelines
Annotates genomic data with allele and genotype frequency, functional impact predictions, evolutionary conservation scores and pathogenicity
Supports all major NGS technologies (Illumina, Ion Torrent, Pac Bio and Roche 454) and project types
Available on Windows, Mac OS X, Linux, and the Amazon Cloud

“perfect analytical partner for the analysis of desktop sequencing data produced by the ION PGM™, Roche Junior, Illumina MiSeq as well as high throughput systems as the Ion Torrent Proton, Roche FLX, Applied BioSystems SOLiD™ and Illumina® platforms.” runs on Windows, free-standing multi-application package-- SNP/Indel analysis, CNV prediction and disease discovery, whole genome alignment, etc.
Data can be imported from Clinvar, dbSNP, Genbank: http://www.softgenetics.com/PDF/NextGene_UsersManual_web.pdf

Cited in over 3,500 peer-reviewed scientific publications
Workflows for microarray and PCR data include: Gene expression including alternative splicing, miRNA expression, Genome Wide Association Studies, Mother-Father-Child Trio analysis, DNA Copy number including allele specific copy number and Loss of Heterozygosity (LOH), and ChIP, and methylation. Next Generation Sequencing (NGS) workflows include: RNA-Seq, miRNA-Seq, ChIP-Seq, DNA-Seq, and Methylation
Powerful statistics and interactive, publication ready visualizations
Supports all commercial next generation sequencing and microarray file format as well as text files
Can input GEO SOFT files

Installation can be cloud-based or on a local cluster or Linux server
Easy to use point-and-click interface
Takes NGS data (.fastq, BAM, SAM), microarrays (Affymetrix, Illumina) and text files
Supports custom genome builds and annotation databases
Performs base trimming, alignment, quantification, quality analysis, statistics, and visualization
Includes ten fully customizable aligners (Bowtie, Bowtie 2, BWA, GSNAP, Isaac 2, SHRiMP 2, STAR, TMAP, TopHat and TopHat 2)
Applications for RNA-Seq, Small RNA-Seq, WGS/WES, Pathway enrichment, Fusion detection and Variant calling
Allows users to create, save, share, or download analysis pipelines for automated and repeatable analysis
Collaborate with others without transferring data
Integrates microarray and next generation sequencing data

[Golden Helix: SNP and Variation Suite] (http://goldenhelix.com/SNP_Variation/)

used for managing, analyzing and visualizing genotypic and phenotypic data; Features: Genome-wide association studies, genomic prediction, copy number analysis, small sample DNA-Seq workflows, large sample DNA-seq analysis, RNA-seq analysis. Supported files: .txt, excel XLS & XLSX, CEL, CHP, CNT, Illumina, Plink PED, TPED, BED, Agilent files, NimbleGen data summary files, VCF files, Impute2 GWAS files, HapMap format, MACH output, + 50 other formats consumes NCBI data directly

Applications: ChIP-Seq, DNA-Seq, RNA-Seq, DNA methylation; enable personalized medicine,
Mining Stations: Supports all established NGS sequencing platforms- SOLiD, 454 Life Sciences, Genome Analyzer, HiSeq, MiSeq, IonTorrent
Software Suite: can upload sequence of BED files
Genome browser: BED and BAM files, Public data- 1500 BED files available for every user

Open source platform (SaaS), analysis and genome sequencing tools, integrates over 400 genomic analysis open source tools and pipelines, have a private and public cloud version. Features: genomic data visualization, drag and drop interface, accelerated analysis, real-time collaboration
They have a couple modules to do so, and have enabled parts of the sra toolkit

Software product, for clinical genomics professionals, manage, curate, report genomic variation
Has own data library -- data from NCBI

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