We provide computational analysis, software development, and consulting in the following areas:
Animal and Population Genomics
- Population structure and genetic diversity analysis
- Ancestry, breed composition, admixture, and introgression analysis
- Relatedness and kinship estimation
- Inbreeding estimation and runs of homozygosity analysis
- Parentage analysis and pedigree verification
- Genome-wide association analysis (GWAS)
- Genotype imputation
- Genomic selection and marker-assisted breeding analysis
- Genotype panel design
- Integration of genomic data with phenotype, health, production, and management records
- Conservation genomics analysis
- Genomic traceability and identity system design
- Low-coverage whole-genome sequencing analysis for ancestry, population genomics, and screening applications
Microbial and Metagenomic Analysis
- Bacterial genome assembly and annotation from client-provided sequence data
- Comparative bacterial genomics, including SNP and indel analysis
- Microbial metagenomic analysis and metagenome assembly
- Microbial strain characterization and genomic epidemiology
- Phage and plasmid identification and annotation
Sequencing and Variant Analysis
- Quality control for genomic, transcriptomic, and metagenomic data
- Short-read, long-read, and hybrid sequencing data analysis
- Genotyping-by-sequencing analysis
- SNP and indel discovery, genotyping, annotation, and prioritization
- Structural variant and copy-number variant discovery, genotyping, and annotation
- Mitochondrial genome analysis, including deletion and duplication detection
- Causative variant discovery, annotation, and prioritization
- Functional interpretation of candidate variants
- Transcriptomic analysis, including mRNA and miRNA expression
- Genotype data harmonization across sequencing and array platforms
- Genotype orientation and format conversion, including Illumina and Affymetrix formats
- Sanger sequencing data analysis
- Preparation and submission of sequence and variant data to repositories such as NCBI and EBI
Bioinformatics Software and Infrastructure
- Custom bioinformatics software development. Production tools are developed using languages such as Python, R, Rust, Ruby, JavaScript, Perl, and Java.
- Database design and development
- Web server and web application development
- Interactive genome visualization development
- Publication-quality scientific visualization and figure generation
- Reproducible workflow development using Snakemake and Nextflow
- Application containerization. Reproducible software environments are created using Docker and Apptainer/Singularity.
- Bioinformatics workflow deployment and optimization on high-performance computing systems
- Maintenance and modernization of existing bioinformatics software and web platforms
Consulting, Data Management, and Training
- Study design and bioinformatics analysis planning
- Bioinformatics troubleshooting
- Computational resource, processing, and storage estimates for research proposals
- Research data management planning
- Metadata and file organization standards
- Reproducibility and workflow review
- Genomic data governance guidance
- Expert review and interpretation of genomic results
- Expert witness services involving bioinformatics, DNA evidence, or genotyping
- Customized training in bioinformatics, Python, R, Bash, workflow development, and high-performance computing