Genomic Data Analysis with OmicsLogic: Empowering Your Research

Introduction

Genomic data analysis is essential for understanding the complexities of genetic variations and their implications in health and disease. However, the intricate processes involved, from preprocessing to variant calling and phylogenetic analysis, require sophisticated tools and expertise. At OmicsLogic, we offer comprehensive genomic data analysis services, leveraging advanced tools and the T-Bioinfo platform to streamline your research process and ensure accurate, reliable results. Here’s how we can assist you at every step of your genomic data analysis journey.

1. Data Preprocessing: Ensuring Quality from the Start

Preprocessing is a critical first step in genomic data analysis, aimed at improving the quality of raw sequencing reads. Our services include:

Analysis Types

• Quality control
• Adapter trimming
• Removal of low-quality bases
• Cleaning PCR artifacts

Tools

• FastQC: Provides quality control for high-throughput sequence data, identifying potential issues in your sequencing data.
• TrimGalore: Applies consistent adapter and quality trimming, crucial for removing adapter sequences and low-quality bases.
• PCR Clean: Cleans PCR artifacts from your data.
• Trimmomatic: Trims low-quality bases and adapter sequences, enhancing the quality of data input for analysis.

Customization: Change parameters for trimming and quality thresholds directly on our server.

2. Mapping: Precision Alignment of Reads

Accurate mapping of sequencing reads to a reference genome is vital for downstream analyses. We provide:

Analysis Types

• High-throughput read mapping
• Genome alignment
• Visualization of mapped reads

Tools

• BWAmem: Optimized for speed and accuracy, ideal for large datasets.
• BWAalign: Provides precise alignment of reads to the reference genome.
• Bowtie2: A fast and memory-efficient tool for aligning sequencing reads to long reference sequences.
• JBrowser SAM file: Visualization tool for mapped reads, aiding in the interpretation of alignment results.

Customization: Adjust alignment parameters such as seed length, mismatch tolerance, and more directly on our server.

3. Variant Calling: Identifying Genetic Variants

Variant calling is crucial for identifying and understanding genetic variations. Our services include:

Analysis Types

• Mutation detection
• Confidence interval estimation
• Comprehensive variant discovery

Tools

• PernculBasic Mutations: Basic mutation detection.
• ConfInterval Binom95: Confidence interval estimation for variant detection.
• GATK: Comprehensive variant discovery toolkit.
• FreeBayes: Bayesian genetic variant detector for accurate and robust variant calling.
• EBCall: Empirical Bayesian approach to variant calling for enhanced sensitivity and specificity.

Customization: Modify detection thresholds and parameters to suit your specific needs.

4. Differential Variant Calling: Comparative Analysis of Variants

Comparing genetic variants between samples provides insights into genetic differences and their potential impacts. We offer:

Analysis Types

• Differential mutation analysis
• Somatic point mutation detection
• Joint inference of single nucleotide variants

Tools

• Diff Mutation: Differential mutation analysis to identify significant differences between samples.
• MuTect2: Sensitive detection of somatic point mutations, particularly useful in cancer genomics.
• JoinSNVMix: Bayesian method for the joint inference of single nucleotide variants.
• SomaticSniper: Identification of somatic point mutations for comparative analysis.
• MutD: Comprehensive mutation detection tool.
• Strelka: Small variant calling optimized for high sensitivity.

Customization: Tailor parameters for mutation detection and comparative analysis on our server.

5. Segmentation: Understanding Genomic Regions

Segmentation involves dividing the genome into regions based on certain criteria. Our services include:

Analysis Types

• Genome segmentation per sample
• Combining segmented regions across samples
• Functional annotation of segmented regions

Tools

• Per Sample Segmentation: Segmenting the genome on a per-sample basis.
• Combine Islands Across Samples: Combining segmented regions across different samples to identify common features.
• Annotation: Annotating the segmented regions for functional insights.

Customization: Adjust segmentation parameters and criteria on our server.

6. Post Processing: Enhancing Data Usability

Post processing is essential for converting and visualizing variant data for further analysis. We provide:

Analysis Types

• Conversion of VCF files
• Visualization of variant data

Tools

• vcf2perncul: Conversion of VCF files for further processing and analysis.
• Variant Visualization: Visualization of variant data to facilitate interpretation and reporting.

Customization: Adjust visualization settings to best display your data.

7. Phylogenetic Analysis: Understanding Evolutionary Relationships

Phylogenetic analysis helps understand the evolutionary relationships between different sequences. Our services include:

Analysis Types

• Preprocessing NGS data
• Mapping NGS data
• Sequence retrieval
• Multiple sequence alignment
• Phylogenetic tree construction
• Post processing and visualization

Tools

• CleanPrimer: Removal of primer sequences from raw reads.
• PCR Clean: Cleaning PCR artifacts.
• Trimmomatic: Trimming low-quality bases and adapter sequences.
• Bowtie2: Efficient read alignment.
• BWA: Genome alignment.
• Visualization: Tools for visualizing mapped reads.
• Shorah: Haplotyping tool for viral populations.
• Perncul: Sample consensus genome generation.
• Multiple Sequence Alignment: Aligning multiple sequences.
• Multiple Sequence Alignment AA: Aligning amino acid sequences.
• Select codon-position MSA: Specific alignment based on codon positions.
• Ape: Phylogenetic analysis and evolution.
• BEAST: Bayesian evolutionary analysis.
• TreeSpace: Visualization of phylogenetic tree space.
• Msa View: Visualization of multiple sequence alignments.

Customization: Modify parameters for each step of phylogenetic analysis on our server.

Flexible Access: Perform phylogenetic analysis using research licenses, FTP file transfers, and SVL links on our server, no HPC required.

Flexible Access for Researchers

At OmicsLogic, we provide comprehensive genomic data analysis services, handling complex analyses with precision and expertise. However, we understand that some researchers prefer to conduct their analyses independently. That’s why we offer flexible access options:

Research Licenses

Researchers can obtain a research license to use our advanced T-Bioinfo platform for their analyses. This license grants access to all the tools and pipelines necessary for genomic data analysis.

FTP File Transfers and SVL Links

Researchers can easily transfer their data via FTP and utilize SVL links to access our server. This ensures a seamless and efficient workflow, allowing for hassle-free data handling.

No HPC Required

Our platform is designed to handle intensive computational tasks without the need for high-performance computing (HPC) resources. This makes our services and tools accessible to researchers with varying levels of computational infrastructure.

By offering these flexible access options, OmicsLogic empowers researchers to perform high-quality genomic data analysis on their own terms, ensuring that they have the support and tools needed to succeed.

Partner with us to unlock the full potential of your genomic data and drive your research forward. Contact us today to learn more about our services and how we can support your research endeavors. Visit our Research Services page for more information.

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