Overview of Support Services
We offer customized consulting sessions to address specific questions and identify gaps that might prevent you from achieving your goals. In these sessions, we can specifically help you with:
- Experimental design for RNA-seq, metagenomics, amplicon sequencing, and whole-genome sequencing experiments
- Soil microbiome experimental design, including field, greenhouse, and microcosm studies
- Selection of appropriate controls, treatments, biological replicates, and sampling strategies
- Soil, rhizosphere, root, and plant-associated microbiome sampling design
- Selection of suitable sequencing platforms, sequencing depth, and library preparation methods
- 16S rRNA, ITS, shotgun metagenomics, and meta transcriptomics study planning
- Experimental design for microbial diversity, community composition, and functional profiling
- Integration of microbiome data with soil physicochemical properties, plant traits, and environmental variables
- Identification and reduction of potential sources of bias, batch effects, and contamination
- Power analysis, sample-size estimation, randomization, and blocking strategies
- Bioinformatics workflow selection and statistical analysis planning
- Interpretation and visualization of microbiome and sequencing results
- Preparation of methods, data-analysis plans, grant proposals, and research manuscripts
Our Expertise
Together, we tailor computational and statistical needs for your project. We help you choose the software you need for your data and streamline the process.
We assist with data curation, organization, integration, quality control, and preprocessing to ensure high data integrity before analysis.
We will structure and analyze your data using the latest bioinformatics methodologies. Whether your question concerns differential gene expression or the development of machine learning models, we will advise or collaborate with you.
Goals are defined before each project starts. We can advise you on which formats would be best for presenting your results for publication, or, as a collaboration, we can deliver your results in your preferred format—Excel tables, Illustrator-friendly vector graphics, dashboards, or manuscripts.
We can also assist with figure preparation, professional PowerPoint presentations, and manuscript-ready outputs.
We can help you write methods and generate graphics.
Tailored training sessions for students, researchers, and corporate teams on bioinformatics tools, data analysis pipelines, and best practices in computational research.
Unlimited email/phone consultations for those seeking advice or follow-up analyses, and ongoing project support until completion as part of collaborations.
As part of collaborations, we can help write methods sections, prepare supplementary data, and ensure reproducibility for peer-reviewed publications or funding proposals.
Bioinformatics Consulting Process
STEP 1
Initial Consultation
Meeting, phone call, or teleconference to discuss your project & scope
STEP 2
Estimate & Timeline
We compile a project proposal for your evaluation
STEP 3
Accept or Reject
The proposal is up for your review and consideration
STEP 4
Bioinformatic support
We develop the methods for data, analyze it, and generate figures
STEP 5
Delivery
We provide a complete project report and outputs
Getting Started
For researchers interested in our bioinformatics services, we recommend beginning with an initial consultation to discuss your project’s goals and specific requirements. Our team will collaborate closely with you to develop a customized analysis plan, including recommendations for optimal sequencing workflows, data processing strategies, and analysis pipelines.
Consultations are currently held virtually/in person, and a ticket/email is required to receive the Zoom link. Don't hesitate to get in touch with chanda.trivedi@ttu.edu to request software installations, server accounts, or appointments for consultations on new projects.
For external users, a fee-based service can be provided that will depend on the nature and complexity of the analysis requested.
We are continuously expanding our bioinformatics services to better support our vibrant
research community. We look forward to assisting with your projects and helping transform
complex data into meaningful insights!
Contact Us
Chanda Trivedi, Ph.D.
Research Assistant ProfessorIGCAST Conference Room 203, Experimental Sciences Building II
Drop-ins are welcome on Tuesdays and Thursdays from 10-11am.
Examples of Deliverables for Data Analysis
We perform comprehensive whole-genome sequencing analysis, which includes raw data quality control and reporting, sequence alignment and variant calling, and detailed annotation of single-nucleotide variants (SNVs), insertions and deletions (indels), and structural variants. Our analysis further covers copy number variation detection, phylogenetic profiling, and population-level variant frequency estimation, where applicable.
To provide biological context, Functional interpretation is provided through gene and pathway annotation, and our findings are delivered in clear, publication-ready reports, tables, and figures.
We carry out in-depth RNA-Seq analysis, including raw data QC, read alignment, and quantification of gene and transcript expression levels.
Our workflow includes differential gene expression analysis with statistical validation, detection of alternative splicing, and isoform profiling. We also perform functional enrichment analyses (GO, KEGG), with outputs summarized through high-quality visualizations such as heatmaps, volcano plots, and PCA.
This service includes raw data QC, alignment and mapping summaries, peak identification with annotation, and differential gene expression analysis.
Functional enrichment analyses (GO, KEGG) provide biological context, and results are delivered with clear visualizations and detailed reports suitable for publication or presentation.
We provide group-wise or individual OTU clustering, abundance reports, and taxonomic annotation (genus level).
Outputs include OTU FASTA files and visual representations, such as pie charts of the top 10 taxonomic classifications (from phylum to species level).
We perform microbiome sequencing analysis, which includes raw data quality control and preprocessing, taxonomic classification of microbial communities, and diversity analyses at both alpha and beta levels. Our workflow further covers differential abundance testing, functional profiling of microbial genes and pathways, and correlation analyses with host or environmental factors.
To ensure clear interpretation, we generate high-quality visualizations such as bar plots, heatmaps, ordination plots, and network diagrams. All results are compiled into detailed, publication-ready reports, tables, and figures that provide actionable biological insights.
Institute of Genomics for Crop Abiotic Stress Tolerance
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Address
Texas Tech University, Institute of Genomics for Crop Abiotic Stress Tolerance, 1006 Canton Ave, Lubbock, TX 79409 -
Phone
806.742.3417 -
Email
IGCAST.info@ttu.edu