GeneSpring NGS Software by Agilent Technologies

Agilent’s GeneSpring NGS software suite includes data analysis workflows for Methyl-Seq, RNA-Seq, DNA-Seq, Chip-Seq and Small RNA-Seq data. GeneSpring NGS provides SureSelect customers with an easy to use QC, visualization and reporting tool for Methyl-Seq, RNA-Seq and DNA-Seq applications. GeneSpring NGS also allows the detection of transcriptomic changes like splice variants and gene fusions, or identify structural variation from whole genome or target enriched samples. Small RNA-Seq allows for the measurement of expression levels of known small RNA genes, mature miRNA and the detection of novel genes. GeneSpring provides comprehensive visualization, data management, and genomic annotations all in one place.

GeneSpring NGS support SureSelect sequencing applications for Methyl-Seq, DNA-Seq, RNA-Seq as well as whole genome application for Methyl-Seq, DNA-Seq, RNA-Seq, ChIP-Seq and Small RNA-Seq with a special emphasis on read, mapping, and library quality control:

• Import of aligned read sequences from Illumina, ABI and 454 (Roche) sequencing platforms
• Import of aligned NGS data in SAM, BAM, and vendor formats like Illumina's ELAND format (in either compressed or uncompressed forms).
• Support for Single End, Paired End and Mate Pair library types
• Interactive QC module for whole genome and SureSelect target enrichment QA/QC
• Automated sample QC report generation

Methyl-Seq analysis features include:
• Enhanced Quality Control Manager for SureSelect
• SureSelect Target Region QC
• Enhanced Genome Browser and Visualizations
• Bisulfite Conversion Error Rate Computation
• Methylation Detection Algorithm
• Lollipop Plot
• Differentially Methylated Cytosines Algorithm
• Differentially Methylated Regions Analysis Algorithm
• Intra Sample Analysis
• Methylation Effect Analysis
• Translate Target Regions to Genes
• Pathway Analysis

DNA-Seq analysis features include:
• Enhanced Quality Control Manager for SureSelect
• SureSelect Target Region Filtering
• Enhanced Genome Browser and Visualizations
• SNP Detection through built-in Bayesian SNP calling algorithm (MAQ)
• Differential SNP Analysis
• Effects of SNPs on transcripts
• Structural Variation (SV) Detection through built-in PEMer and k-BIC algorithms
• Translate Target Regions to Genes
• Pathway Analysis

RNA-Seq analysis features include:
• Enhanced Quality Control Manager for SureSelect
• SureSelect Target Region Filtering
• Enhanced Genome Browser and Visualizations
• Differential Expression Analysis
• T-Test
• Anova
• Identification of differential splice variant by Expectation-Maximization (EM)
• Gene Fusion Analysis
• Identification of novel exons and splice junctions
• Quantification with Novel Detection Report
• RPKM Filtering
• Pooled Analysis
• Z-test
• Audic-Claverie test
• Clustering
• PCA
• Pathway Analysis

Small RNA-Seq analysis features include:
• Enhanced Quality Control Manager
• Enhanced Genome Browser and Visualizations
• Quantification
• Expression Analysis
• TargetScan, TarBase, PicTar, PITA and microRNA.org databases available for targeted genes and miRNA identification
• Validation of Mature RNA Annotation
• Pathway Analysis