High Performance Pipelines for NGS Data Analysis
  1. Haplotype-based DNA Variant Detection Analysis and new function of project data sharing are now supported by HiPipe Profrssional (10 May 2016).
  2. RNA Variant Detection Analysis is now available in HiPipe Profrssional (3 Feb 2016).
  3. A new version of HiPipe supporting multiple-sample analysis and data management is open for beta testing (25 Nov 2015).
HiPipe provides high performance NGS data analysis pipelines with intuitive user interface to the community so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task. Please see Info for details.
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DNA Analysis
Whole Genome & Exome Variant Detection
Pipelining raw sequences into BWA for mapping and then into GATK for variant detection. Usually, a human exome (100x) can be processed in one hour or so.
De novo Assembly
Based on Velvet 1.2.10, this pipeline currently accepts only paired-end reads and optional long single-end reads.
Exome CNV Detection (Experimental)
RNA Analysis
Differential Expression Analysis
Pipelining raw sequences into TopHat for mapping and then Cufflinks for differential expression. Usually, 12*2 Gbp (paired samples, human) rna-seq data can be processed in about 2-5 days or so.
Gene Fusion Detection
Pipelining raw sequences into TopHat-Fusion for mapping and searching candidate fusion genes. Usually, the analysis for 900Mbp (paired samples, human) of transcriptome data requires about 2 hours.
miRNA analysis
Filtering out contaminants and using miRDeep2 for miRNA profiling.
Variant Detection (Experimental)