De novo assembly reconstructs the genome from scratch without using a reference, ideal for novel strains or discovering structural variations. Reference-guided assembly aligns reads to a known reference genome, providing faster analysis and better contiguity for well-characterized organisms.

We analyze all bacterial species including clinical isolates, environmental bacteria, extremophiles, and novel species. Our pipelines are optimized for both gram-positive and gram-negative bacteria with varying GC content and genome sizes.

Complete deliverables include assembled genome files (FASTA), annotation files (GFF/GBK), quality reports, AMR/virulence analysis results, phylogenetic trees, and a comprehensive PDF report with biological interpretation and visualizations.

We analyze diverse samples including soil, water, sediment, gut microbiome, oral microbiome, skin microbiome, plant rhizosphere, and clinical specimens. Each sample type requires specific preprocessing considerations.

We use comprehensive databases including NCBI RefSeq, GTDB, ChocoPhlAn, UniRef, KEGG, COG, CAZy, and specialized databases for antibiotic resistance genes and virulence factors.

We typically use FDR < 0.05 and |log2FC| > 1 as default thresholds, but these can be adjusted based on your experimental needs and biological context. We provide both raw p-values and corrected p-values.

Yes, we handle multi-factor designs, time-course experiments, paired samples, batch effects, and other complex scenarios using appropriate statistical models and design matrices.

We recommend 100x average coverage for clinical applications and 50x for research. Higher coverage improves variant calling sensitivity, especially for heterozygous variants and CNVs.

Yes, we specialize in trio analysis (proband + parents) for de novo variant detection and cohort analysis for case-control studies, including population stratification and association testing.

We accept gene symbols, Ensembl IDs, RefSeq IDs, UniProt IDs, and Entrez Gene IDs. We can also work with differential expression results including fold changes and p-values for more sophisticated analyses.

Yes, we perform orthology-based analysis for non-model organisms by mapping genes to well-annotated species (human, mouse, fly, etc.) and can create custom pathway databases for specific organisms.

V3-V4 region is most popular for balanced taxonomic resolution. V4 region offers good cost-effectiveness, while V1-V3 is better for specific applications. We can advise based on your sample type and research goals.

Yes, we specialize in longitudinal analysis including time-series modeling, trajectory analysis, and identification of temporal patterns in microbial communities using specialized statistical approaches.

We provide high-resolution formats including PDF, SVG, PNG (300+ DPI), and EPS for publications. All figures are designed to meet journal requirements with proper sizing, fonts, and color schemes.

Yes, we provide well-documented R/Python scripts for all visualizations, enabling you to reproduce, modify, and adapt the plots for future analyses or different datasets.

We accept all standard Sanger sequencing formats including AB1, SCF, ZTR trace files, and FASTA/FASTQ sequence files. We can also process batch uploads of multiple files.

Yes, we have automated pipelines for processing hundreds to thousands of Sanger sequences with batch reporting and statistical summaries across entire datasets.

We typically require at least 50-100 bp overlap with >95% identity for reliable assembly, though parameters can be adjusted based on sequence quality and project requirements.

We provide primer design recommendations for walking strategies to extend sequences and close gaps, including optimal primer positioning and conditions.

We can detect SNPs, small INDELs (<50 bp), heterozygous variants, and complex variants from Sanger sequencing data. Large structural variants require specialized analysis approaches.

Absolutely! We can analyze segregation patterns in families, determine inheritance modes, and provide genetic counseling recommendations based on variant data.

We provide expert manual review combined with automated tools, identifying subtle artifacts and mixed sequences that automated systems might miss, ensuring highest accuracy.

We provide detailed PDF reports with annotated chromatograms, quality metrics tables, sequence summaries, and recommendations in both technical and client-friendly formats.

Nextflow excels for cloud deployment and complex dataflows, while Snakemake is ideal for Python-integrated workflows and HPC environments. We'll recommend the best fit for your specific use case.

Yes, we offer comprehensive training on workflow development, best practices, and ongoing support for pipeline maintenance and optimization.

Docker is ideal for development and cloud deployment, while Singularity is preferred for HPC environments due to security requirements. We often provide both formats for maximum compatibility.

Yes, we can set up Kubernetes, Docker Swarm, or workflow-based orchestration systems for complex multi-container applications and scalable deployments.

Cost depends on your specific workload. We analyze your requirements and provide cost comparisons across platforms, often recommending hybrid approaches for optimal pricing.

Absolutely! We provide complete migration services including dependency mapping, containerization, data transfer strategies, and gradual migration approaches to minimize downtime.

Improvements vary by pipeline complexity, but we typically achieve 2-10x speedup through parallelization, algorithm optimization, and resource management improvements.

We provide detailed before/after benchmarks including runtime, resource utilization, cost metrics, and throughput measurements with comprehensive performance reports.

R Shiny is excellent for bioinformatics with rich package ecosystem, while Python Dash offers modern web features and ML integration. We choose based on your data pipeline and team preferences.

Absolutely! We provide comprehensive training on dashboard management, updates, and basic customizations so your team can maintain and extend the applications.

We provide vector formats (PDF, SVG, EPS) for scalability and high-resolution raster formats (PNG, TIFF) at 300+ DPI for journal requirements. All formats are publication-ready.

Yes, we provide well-documented, reproducible code (R/ggplot2 or Python/matplotlib) that allows you to regenerate and modify figures for future publications or revisions.

We work with standard formats including VCF, BAM/SAM, BED, GFF/GTF, BigWig, and various genomic annotation formats. We can also convert between formats as needed.

Absolutely! We can create custom genome browsers using tools like JBrowse, IGV.js, or completely custom solutions tailored to your specific genomic data and visualization requirements.

We use modern web technologies including React, Vue.js for frontend, Python/Django, R/Shiny for backend, and can integrate with databases, APIs, and cloud services as needed.

Absolutely! We offer maintenance plans including bug fixes, security updates, feature enhancements, and technical support to ensure your tools remain functional and current.

No prior experience required! We offer beginner-friendly courses that start from basics. We also have advanced tracks for experienced programmers wanting to specialize in bioinformatics applications.

Yes! All participants receive comprehensive training materials, code examples, datasets, and completion certificates. Materials remain accessible for future reference and practice.

Workshops are highly interactive with 70% hands-on analysis using real datasets. Each participant works through complete analysis pipelines with guided instruction and troubleshooting support.

Advanced workshops include sessions for analyzing participant data with personalized guidance. We recommend starting with provided datasets for foundational workshops.

Basic algebra and calculus knowledge is helpful but not required. We focus on conceptual understanding and practical application rather than mathematical derivations.

Absolutely! We cover proper statistical reporting, figure preparation, and how to communicate statistical results effectively in scientific publications.

We work with academic research projects, biotech startups, pharmaceutical companies, and government agencies on projects ranging from basic research to translational studies and clinical applications.

Engagements range from single-day strategic sessions to multi-month project support. We customize the scope and duration based on your specific needs and project complexity.