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BIRAC-SciGenom High Performance Computing Infrastructure

Introduction

The recent advancement in sequencing technologies is revolutionizing biomedical and clinical research. It is also radically changing the crop and animal science research. Several next generation sequencing (NGS) platforms have been developed including by Illumina, 454, LifeTechnologies, PacificBio and others, that generate huge are large amount of sequence data in short amount of time. For example the Illumina HiSeq 2000 can generate 600 Gb of data sequence data in roughly two weeks time.

It is the equivalent of 200x coverage of haploid human genome. The NGS approach in addition to sequencing/resequencing normal genomes is applied to sequencing cancer genomes, exomes, transcriptomes, metagenomes and epigenomes. In the past generating this large amount of data would took years and give that it can be done in a matter of weeks, it has produced new challenges and opportunities in regards to data storage, retrieval and analysis.

Currently, a major limitation in computational infrastructure is one of the main rate-limiting factors in being able to leverage the NGS technologies. Each type of NGS data generated requires different levels of computational resources. For e.g., the de novo assembly of transcriptome data (i.e. assembling transcriptome data for species where there is no reference genome) and de novo genome (or assembling new genomes) requires both huge amount of memory and computing power to assemble and annotate the data in a timely fashion.

Whereas, the human re-sequencing and human exome data analysis though algorithmically not challenging, timely (or real time) delivery of results in a clinical setting for treatment decisions, demand significant investment in computational resources.

About Facility

The facility will provide state-of-art computing and storage resources needed by the next-generation sequence data projects. It will help SciGenom scientists and programmers to run next-generation sequence analysis pipelines and programs efficiently. The facility will also provide an unique opportunity to the researchers at SciGenom to develop efficient and faster programs and pipelines for next-generation data analysis.

The high-performance computing (HPC) and storage infrastructure will provide analysis facility for next-generation sequencing data to academic institutions and research labs. The data analysis services will be provided at discount price (25%) to government and academic institutions.

The infrastructure will also host our in-house developed bioinformatics tools and databases, which will be free for government-aided institutions. The facility will encourage SciGenom researcher and research institutions to collaborate on project of national importance. The facility will help India in the area of computational genomics and biomedical research.

Infrastructure

List of NGS Analysis Services

Model - I Model - II
Reference-based whole genome analysis (FastQC+CutAdapt+BWA+Picard+Samtools+ Vep) Reference-based whole genome analysis (FastQC+CutAdapt+BWA+Picard+Samtools+VeP)
Reference-based RNA-seq analysis (FastQC+CutAdapt+HISAT+Cufflinks) Reference-based RNA-seq analysis (FastQC+CutAdapt+HISAT+Cufflinks)
Reference-based RNA-seq analysis (FastQC+CutAdapt+TopHat2+Cufflinks) Reference-based RNA-seq analysis (FastQC+CutAdapt+TopHat2+Cufflinks)
Reference-based RNA-seq analysis (FastQC+CutAdapt+STAR+Cufflinks) Reference-based RNA-seq analysis (FastQC+CutAdapt+STAR+Cufflinks)
Reference-based whole exome analysis (FastQC+CutAdapt+BWA+Picard+Samtools+VeP)
Denovo trancriptome analysis (FastQC+CutAdapt+Trinity+BLASTX+Bowite2+DESeq2)
Denovo trancriptome analysis (FastQC+CutAdapt+SOAPdenovoTrans+BLASTX+Bowite2+ DESeq2)
Denovo Genome Assembly (Smaller Genome)*
Model - I = Bioinformatics analysis component of NGS (Next Generation Sequencing) projects - Under this model the bioinformatics services will be extended to those customers, who perform their sequencing with SciGenom.
Model - II = The customer can send the sequenced data to SciGenom for performing data analysis. SciGenom will decide on complete analysis after assessing the data quality. If the data fail the quality parameters then the customer need to pay for quality assessment per sample.

Pricing for NGS Analysis Services

Please write to raju.v@scigenom.com for BIRAC affiliated projects.

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