Zynt Bio delivers cloud-native, high-performance computational genomics services optimized exclusively for plant systems, environmental microbiomes, and industrial biomanufacturing. By deploying containerized Nextflow workflows natively on enterprise-grade AWS cloud infrastructure, we guarantee 100% reproducible, audited, and scalable data processing.
1. Functional Transcriptomics & Regulatory RNA-Seq
We provide high-resolution mapping, quantification, and deep biological profiling of cellular coding and non-coding RNA dynamics.
- Differential Gene Expression (DGE): Comprehensive transcriptomic profiling optimized for complex multi-factor agricultural matrices, time-course fermentation studies, and multi-genotype systems utilizing advanced nf-core/rnaseq frameworks.
- Small RNA & RNA Interference (RNAi) Profiling: Specialized workflows (nf-core/smrnaseq) tailored for identifying and quantifying small RNA populations, microRNAs (miRNAs), and target gene-silencing efficiency.
- Functional Annotation & Metabolic Pathway Enrichment: Moving beyond raw gene IDs. We execute deep Gene Ontology (GO) mapping, KEGG/EggNOG pathway reconstructions, and functional network modeling to trace active biochemical mechanisms.
2. Host-Pathogen Crosstalk & Environmental Metagenomics
Specialized workflows designed for highly diverse, complex ecosystems where separating host, vector, and microbial sequence profiles is computationally critical.
- Dual RNA-Seq Processing: Simultaneous alignment and de-convolution of interacting organisms (e.g., plant-fungal, plant-bacterial, or host-pest systems) to isolate host immune pathways from pathogen virulence factors.
- Shotgun Metagenomics & Functional Profiling (Terra-Meta): Deep functional assessment of soil, rhizosphere, or plant-associated microbiomes. We map environmental DNA (eDNA) directly to metabolic pathways to profile community capacity (e.g., nitrogen fixation, phosphate solubilization).
- Metagenome-Assembled Genomes (MAGs) & Binning: Extracting near-complete, independent draft chromosomes of unculturable, novel environmental microbes directly from complex substrate matrices utilizing advanced binning tools (MetaBAT2, MaxBin2).
- High-Throughput Amplicon Sequencing (16S / ITS / 18S): Standardized microbial community profiling (nf-core/ampliseq) to monitor population and taxonomic shifts across treatments, inoculants, or environmental changes over time.
3. Industrial Biotech Strain Verification & Quality Control
Tailored for synthetic biology, crop-protection R&D, and biomanufacturing organizations looking to audit genomic stability.
- Whole-Genome Resequencing & Variant Calling: High-depth DNA alignment (nf-core/sarek) against parent references to discover single nucleotide polymorphisms (SNPs), short insertions/deletions (InDels), or large structural rearrangements.
- CRISPR/Cas9 Off-Target Mutation Screening: Strict structural analysis following gene-editing protocols to verify genomic stability and guarantee zero unintended edits outside the target locus.
- Plasmid & Expression Cassette Integrity Audits: High-depth sequencing verification to confirm that engineered plasmids or multi-gene metabolic cassettes have integrated flawlessly into production strains without truncation or sequence drift.
- De Novo Reference Assembly & Annotation: Building continuous, circularized bacterial chromosomes or highly contiguous fungal scaffold assemblies from scratch for non-model organisms, complete with fully structural structural and functional annotation flags (Bakta, Funannotate).
Deliverables Included with Every Project
Comprehensive Synthesis Portfolio
A clear executive and technical report interpreting the biological relevance, metabolic impacts, and actionable outcomes of your dataset.
Interactive Data Explorer Dashboards
Web-accessible, secure visualization environments hosted via private AWS client portals, allowing your team to dynamically filter genes, explore volcano plots, and extract raw data matrices.
Technical Methodology & IP Documentation
A rigorous, formal narrative detailing exact computational steps, database versions, and command-line parameters. This technical narrative is structured specifically for corporate legal and R&D teams to support internal research records, patent applications, and intellectual property defense.
Standardized R&D Methods & Regulatory Reporting
A compliance-grade report breaking down data ingestion criteria, alignment constraints, and statistical validation thresholds. This document is engineered for immediate integration into corporate technical reports, standard operating procedures (SOPs), or regulatory compliance dossiers.
Auditable Nextflow Traceability Logs
Full workflow metadata files including container hashes, software version pinning, and time-stamped execution logs down to the millisecond (-with-report HTML logging) to guarantee absolute transparency and computational reproducibility.
Secure Cloud Storage Assets
Cleaned FASTQ files, BAM alignments, quantified count matrices, and high-resolution figures safely archived in an isolated Amazon S3 bucket, accessible exclusively by your organization.