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Service

This section provides basic information about Service

Bioinformatics

Overview

Professional bioinformatics support has become an essential part of any NGS based Genomics study. DNA Link’s bioinformatics service is designed to assist researchers in areas of difficulties, such as Bio-IT, statistics, and data mining. Service is divided into Standard and Advanced service, and customized service is also available for cost-effective research.

We, DNA Link, have been involved in numerous government funded projects and recognized for our technical prowess in genomics through papers. Also, by implementing the nation’s first EMC isilon NAS Storage 1.5PB, we have built an automatic system of next generation sequencing infrastructure, and the optimal service environment with the help of 1,000 CPU core analysis server.

Service Type
Basic analysis
Advanced analysis
Exome Capture Sequencing
  • Raw data delivery using downloadable link or hard drive devices
  • Analysis using GATK(2.7) best practices guideline
  • Alignment to reference sequence(hg19/b37.2) using BWA(.bam)
  • SNP and short INDEL will be hard filtered to GATK recommendations(.vcf)
  • Sequencing Summary(.xlsx)
  • Alignment Summary(.xlsx)
  • Depth Coverage Plot(.xlsx)
  • Genotype Calling and SNP detection
  • Germline & Somatic Variant Summary and Annotation(.xlsx)
  • Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster)
  • Frequency estimation using 1000genome and ESP4500
  • NGS-GWAS Analysis
  • Rare Variants Analysis
  • Gene Cluster Annotation(GSEA, KEGG pathway)
  • Customized Analysis(Client Support)
Whole Genome Sequencing
  • Analysis using GATK(2.7) best practices guideline
  • Sequencing Summary
  • Alignment Summary
  • Depth Coverage Plot
  • Genotype Calling and SNP detection
  • Germline & Somatic Variant Summary and Annotation
  • Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster)
  • Frequency estimation using 1000genome and ESP4500
  • NGS-GWAS Analysis
  • Rare Variants Analysis
  • Gene Cluster Annotation(GSEA, KEGG pathway)
  • Fusion gene analysis
  • CNV analysis
  • Customized Analysis(Client Support)
Target Region Capture Sequencing
  • Analysis using GATK(2.7) best practices guideline
  • Sequencing Summary
  • Alignment Summary
  • Depth Coverage Plot
  • Genotype Calling and SNP detection
  • Variant Summary and Annotation
  • Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster)
  • Frequency estimation using 1000genome and ESP4500
  • NGS-GWAS Analysis
  • Rare Variants Analysis
  • Gene Cluster Annotation(GSEA, KEGG pathway)
  • Customized Analysis(Client Support)
De novo Assembly
  • Sequencing Summary
  • Pre-Assemble ( Error correction )
  • De novo Assembly ( contig, scaffold )
  • Consensus Polishing
  • Gene prediction ( need RNA-seq data for Eukaryotes )
  • Genome plot
  • De novo Assembly (contig, scaffold)
  • Gene Annotation (Gene Ontology)
  • Customized Analysis (Client Support)
mRNA Sequencing
  • Sequencing Summary
  • Alignment Summary
  • Summarizing plots
  • Density plot, Box plot, GSEA, Scatter plot, Volcano plot
  • List of genes expressed differentially between given classes
  • List of transcripts expressed differentially between given classes
  • Pathway analysis using DAVID
  • Fusion gene analysis
  • Customized Analysis
smallRNA Sequencing
  • Sequencing Summary
  • Alignment Summary
  • Visualization plot
  • Density plot, Box plot, GSEA, Scatter plot, Volcano plot
  • Targetscan Analysis (limited to specific species)
  • Pathway Analysis
  • Customized Analysis
ChIP Sequencing
  • Sequencing Summary
  • Alignment Summary
  • List of peak positions identified by ChIP-seq tools
  • Input data is transformed into applicable bam or wig format, as needed for visualization by commonly used genome browsers (e.g. IGV or UCSC Genome Browser)
  • Medip analysis
  • Peak analyzer analysis
  • Customized Analysis(Client Support)