Our Bioinformatics Capabilities | MedGenome

Research Services

MedGenome offers end-to-end services for next generation genomics data analysis using proprietary interpretation tools and automated pipelines. Due attention is devoted to each step of the data analysis process.

Our analysis components include quality assessment of raw data, comprehensive data analysis, interpretation of results for biological insights, and presentation of results to the customers in meaningful, easily readable report format.

Further, we optimize all parameters to ensure speedy on-time delivery of finished projects, without sacrificing data quality. Our custom data analysis offering is designed to accommodate your specific requirements and is especially designed to employ publicly accessible datasets along with your own data, as a part of the experimental analysis. For example, we specialize in building custom novel pipelines for our clients whose analysis needs are not addressed with pre-existing pipelines. As a typical case, we have built and offered services for clients to identify foreign DNA insertion sites in eukaryotic genomes. Depending on the type of analysis, our pipelines are capable of delivering robust reliable results, even with partial genome assemblies.

Additionally, as value addition, we offer premium Amazon cloud (AWS) based data analytics services to expedite turnaround time for critical projects. This is particularly useful for projects with a significant scale of samples, such as population genetics projects, where the initial step in analysis engages substantial analytics hardware.

Genome Bioinformatics

Whole Genome Sequencing, Exome Sequencing, Custom DNA Sequencing
Softwares/Pipelines

GATK standard analysis pipeline (CAP compliant)

Bioinformatics Deliverables Included

Variant (SNP, indel) calling and annotation, structural variation (CNV) calling and annotation, gene prediction and annotation, comparative analysis, family analysis, disease analysis

Bioinformatics Deliverables On Request

Prediction AA substitution and risk score, frequency estimation, rare variant analysis, gene cluster annotation

HLA Sequencing

The raw sequence reads are aligned using a FASTA-like algorithm. Instead of aligning the reads to a single reference however, the reads are aligned to all the alleles in the library Analysis of the NGS data involves specialized software algorithms to align hundreds of short oligonucleotide reads to the allele sequences managed by the IMGT/HLA. There is significant variability in the sequence length of alleles in the IMGT/HLA database, as an allele can be named by providing sequence from as little as one exon, while many alleles have full-locus sequences.On Request

Dialogue for custom requirements

Metagenomics

Softwares/Pipelines

Hybrid proprietary pipeline with in-house database and external tools

Bioinformatics Deliverables Included

Genus and species ID, quantification/diversity assessment, differential analysis, dominant population analysis

Bioinformatics Deliverables On Request

Pathway analysis, microbial activity assessment (growth)

Transcriptome Bioinformatics

RNA Sequencing, Custom RNA Sequencing

Softwares/Pipelines DESeq2/TopHat + CuffLinks

Bioinformatics Deliverables Included

DGE, gene abundance quantitation, novel genes and transcripts discovery, gene annotation, gene ontology, gene set enrichment analysis

Bioinformatics Deliverables On Request

Splice site usage for isoforms, pathway analysis using DAVID, gene fusion analysis, allele specific expression

Small RNA Sequencing

Softwares/Pipelines

Small RNA workbench

Bioinformatics Deliverables Included

DGE, quantification, discovery, target prediction, gene ontology, gene set enrichment analysis

Bioinformatics Deliverables On Request

Novel micro RNA discovery, pathway analysis for gene targets

Metatranscriptomics

Softwares/Pipelines

Internal pipeline

Bioinformatics Deliverables Included

Species ID, quantitation, diversity assessment, comparison of diversity across groups, functional analysis of transcripts

Bioinformatics Deliverables On Request

Pathway analysis

Epigenome Bioinformatics

Whole Genome Methylation Sequencing, Focused Methylation Sequencing
Softwares/Pipelines

BISMARK

Bioinformatics Deliverables Included

DMRs profiling and classification, genes associated with DMRs, TSS mapping, gene set enrichment analysis

Bioinformatics Deliverables On Request

Comparison with public databases, employing customer specified public datasets as controls or outgroups, mapping of epigenome markers to known epigenetic modifications, combinatorial analysis of various public datasets for customer specified regions of interest along with customer data

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