High Performance Pipelines for NGS Data Analysis
  1. Genome reference of GRCh38 is supported in Haplotype-based Variant Detection Analysis by HiPipe Professional(30 Jan 2018).
  2. Annotation of genomic variants are available in Low Frequency Variant Detection Analysis and RNA Variant Detection Analysis by HiPipe Professional(28 Nov 2017).
  3. Annotation of genomic variants is supported in Haplotype-based DNA Variant Detection Analysis by HiPipe Professional (25 Sep 2017).
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
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