제품 특징

OmicSoft Suite는 OmicSoft Server와 OmicSoft Studio를 통합한 올인원 솔루션입니다. 중앙 집중식 시스템으로 프로젝트 및 샘플을 안전하게 관리하고, 최신 기술을 이용한 저장, 분석, 관리 및 시각화를 제공하며, Land DB를 이용하여 시간, 비용 및 노력을 절약할 수 있습니다. OmicSoft Server의 클러스터, 클라우드, 그리드 시스템 및 하이브리드 설정에 대한 지원을 포함하여 다양한 NGS 분석, qRT-PCR, CNV, GWAS/Genotyping 분석이 가능합니다.

주요 기능

OmicSoft Suite

• 프로젝트 및 샘플 관리
• Land 분석 및 시각화
• 서드 파티 분석 툴과 연계 기능
• 파이프라인 관리 - GUI 또는 command line 기반 / 프로세스 자동화
• 클라이언트 측 서버에 OmicSoft Server 소프트웨어 설치(클라우드 / 하이브리드 통합)

NGS ANALYTICS (Total)

• FASTQ, Post alignment QC
• Alignment to Genome using OSA
• Gene and Transcript counting using RSEM algorithm
• Exon, exon junction counting
• Post counting normalization methods
• Mutation detection and annotation
• Alternative Splicing Analysis
• Differential analysis using DESeq
• Fusion Detection using FusionMap
• Copy Number detection and segmentation algorithm
• BAM manipulation and export tools
• Integration with Genome Browser, R
• Grid integrated in conjunction with OmicSoft Server
• Run external tools ( Tophat , Cufflinks , and more) in conjunction with
• Configure and run pipelines in conjunction with OmicSoft Server

RNA-seq

• FASTQ QC
• Alignment to Genome using OSA
  • Illumina
  • PacBio
  • IonTorrent
• Post-alignment QC
• Gene and Transcript counting using RSEM algorithm
• Exon counting
• Exon junction counting
• Post-counting normalization methods
• Mutation detection and annotation
• Alternative Splicing Analysis
• Differential analysis using DESeq
• Fusion Detection using FusionMap
• BAM manipulation and export tools
• Integration with Genome Browser
• Integration with R
• Grid-integrated in conjunction with OmicSoft Server
• Run external tools (Tophat, Cufflinks, and more) in conjunction with 
• Configure and run pipelines in conjunction with OmicSoft Server

DNA-seq

• FASTQ QC
• Alignment to Genome using OSA
  • Illumina
  • PacBio
  • IonTorrent
• Post-alignment QC
• Fusion Detection using FusionMap
• Mutation detection and annotation
• Somatic Mutation detection algorithm
• Copy Number detection and segmentation algorithm
• Targeted sequencing analysis
• BAM manipulation and export tools
• VCF manipulation and visualization tools
• Integration with Genome Browser
• Integration with R
• Grid-integrated in conjunction with OmicSoft Server
• Run external tools (BWA, Bowtie, GATK and more) in conjunction with
• Configure and run pipelines in conjunction with OmicSoft Server

Gene expression

• Generic platform importing
  • Affymetrix, Illumina, Agilent, Nanostring, Generic platform
• Normalization modules (RMA, GCRMA, MAS5, Omicsoft Signal Extraction)
• QC and pattern modules
• Clustering (Hiearchical, K-means, PAM, SOM, NMF)
• Correlation to covariates
• Prediction and Classification
• Data manipulation 
  • Transformation (log2, log10, percentile, etc)
  • Combine by gene or sample grouping
• Statistics
  • T-Test
  • ANOVA
  • Repeated Measures
  • General Linear Model Survival Analysis
• Trend Analysis
• Integration with R
• Configure and run pipelines in conjunction with OmicSoft Server

Copy number

• Affymetrix, Illumina, Agilent Platform
• Log2 ratio generation
• B Allele Frequency
• Built in segmentation algorithm
• Summarize at gene or segment levels
• Compatible with Genome Browser
• Integration with Expression data
• Run external tools in conjunction with OmicSoft Server

RT-PCR

• ABI, Biomark, Roche 
• Housekeeper normalization
• Relative abundance calculation
• Delta Ct calculation
• Delta Delta Ct calculation
• Configure and run pipelines in conjunction with OmicSoft Server

Genotyping/GWAS

• QC
• Imputation
• Pattern Detection
  • Linkage Disequilibrium
  • PCA
  • IBS/IBD Estimation
• Single and Two Marker Association
  • Quantified Traits
  • Binary Traits
  • Categorical Traits
  • Survival Traits
  • Repeated Measure Traits
• Integration with R
• Configure and run pipelines in conjunction with OmicSoft Server

연구대상

Human, Animal, Plant, Fungi, Algae, Bacteria

연구분야(추후 수정 예정)

Genome 분석

• 전장유전체 레퍼런스 맵핑
• SNPs 분석
• 바이오 마커 개발
• 유전병 및 질환 연관 변이 분석

Transcriptome 분석

• 표준전사체 어셈블리
• RNA-seq 기반 발현 분석
• small RNA 분석
• Microarray 데이터 분석

특이사항

시스템 요구사항

Requirements

• Baseline memory footprint is dependent on whether or not OmicSoft Lands are hosted on the server (~16GB for OmicSoft Server with all OmicSoft Lands), the numbers of platforms, and on the projects on the server. Additional memory is required for analysis; a single NGS alignment job will take ~12GB memory.
• Most of the 10k+ rpm IDE hard drives (or SCSI drives) have a maximal capacity 400GB.
• Two hard drives are strongly recommended for backup purpose. We suggest a backup at least every week. If one hard drive fails, it only takes one simple configuration change to connect the server to the other hard drive.
• Networking speed between server and clients are largely dependent on the server upload/download speed.

Other Requirements / Suggestions

• The performance of the server is largely determined by the I/O speed. Therefore, we do not recommend USB external hard drives. Local hard drives or file servers are strongly recommended. File servers with parallel I/O support will have the best performance.
• We recommend incremental backup because most of the data managed by the server will not be changed after publishing.
• For OmicSoft Server v. 5.0, Microsoft PowerPoint must be installed.