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