Bacteriophage Genomics Publication Projects Bacteriophage Genomics publication projects cover phage discovery, assembly, annotation, taxonomy, host-range inference, comparative genomics, and therapy candidate safety screening Choose your interested focused area and tap WhatsApp Chat to start a conversation. Our team will guide you through the joining process, fees, timelines, and the documents needed for enrollment.
Focused Areas (Only a few items are shown in detailed view to illustrate the concept)
Chat on WhatsApp
Contact via Whatsapp on +918977624748
Phage Discovery & Isolation Analytics
Phage plaque morphology scoring rubric and image-based QC
Isolation metadata schema and sample-to-phage traceability model
Host panel selection plan for broad host-range screening
Enrichment protocol variables and yield sensitivity analysis design
Time-to-lysis kinetics modeling from turbidity curves
Phage titer normalization and replicate concordance checks
Contamination detection plan for mixed phage preparations
Phage stability testing plan across pH, temperature, and salts
Standardized phage naming convention and accession-ready metadata
Isolation-to-sequencing handoff checklist with chain-of-custody
High-throughput spot assay data model and dashboard
Host growth phase effects on adsorption assay interpretation
Phage burst size estimation workflow with uncertainty reporting
Phage adsorption rate calculation and parameter fitting notebook
QC rules for plaque picking and clonal purification cycles
De-identified sample metadata template for publication tables
Batch effect detection across isolation days and operators
Replication plan for independent isolates and technical repeats
Negative control catalog and false-positive prevention SOP
End-to-end reproducibility pack for discovery experiments
Genome Sequencing, Assembly & QC
Read QC and adapter trimming SOP for phage sequencing runs
Coverage depth diagnostics and low-coverage rescue strategy
Hybrid assembly decision tree for Illumina and long reads
Assembly polishing workflow with error profile reporting
Contig circularization checks and termini inference plan
Genome completeness estimation and contamination screening
Assembly comparison across assemblers with consensus selection
Duplicate read and index hopping detection for phage libraries
Reference-free k-mer QC to detect mixed populations
Variant calling for within-isolate microdiversity tracking
Consensus genome generation with ambiguity masking rules
Assembly graph interpretation guide for repeat-rich regions
Read mapping QC figures: coverage plots and GC bias
Benchmarking assembly metrics across replicate libraries
Quality gates for submission-ready FASTA and metadata
Pipeline containerization for reproducible assembly results
Automated report generation: QC tables and plots
Cross-sample contamination detection using shared k-mers
Genome termini validation using read start enrichment
Final assembly audit checklist for publication
Annotation, Functional Genomics & Modules
Gene calling comparison: Prodigal vs PHANOTATE concordance
Functional annotation workflow using HMM and curated databases
tRNA and tmRNA detection with verification criteria
Promoter and terminator prediction for operon architecture
Phage structural gene module identification and mapping
DNA replication and packaging module annotation framework
Tail fiber and receptor-binding protein annotation playbook
Lysis cassette identification: holin-endolysin-spanin mapping
Anti-CRISPR gene prediction and confidence scoring
Auxiliary metabolic gene screening and ecological interpretation
Mobile element and integrase detection with lifestyle cues
Annotation of small proteins and overlapping genes handling
Manual curation checklist for key hallmark genes
Genome map figure generation with publication styling
Protein domain enrichment analysis across phage groups
Comparative annotation transfer and ortholog validation
Phage proteome completeness score and missing hallmark flags
Functional category summary tables for manuscripts
Annotation error spotting using frameshift and pseudogene rules
Re-annotation workflow for legacy genomes to current standards
Taxonomy, Classification & Phylogenomics
Taxonomic assignment using ICTV-aligned marker strategies
Average nucleotide identity (ANI) computation and thresholds
Average amino-acid identity (AAI) analysis for distant phage sets
Proteomic tree building and bootstrap stability reporting
Whole-genome alignment and conserved block visualization
Gene-sharing network construction using vContact-style methods
Clade definition rules and sensitivity analysis for cutoffs
Genome synteny analysis and rearrangement summary metrics
Pan-genome curve modeling for phage groups
Orthogroup clustering with inflation parameter tuning
Marker gene selection and paralog filtering SOP
Time-scaled phylogeny outline for dated samples (optional)
Host taxonomy overlay on phylogenies and co-phylogeny tests
Recombination detection and masking strategy before tree building
Horizontal gene transfer hotspot mapping across modules
Species demarcation report template with evidence grading
Batch processing pipeline for large phage genome collections
External validation using reference phage genomes and controls
Phylogenomics figure pack: trees, networks, and synteny panels
Reproducible taxonomy appendix with parameters and versions
Host Range, Receptors & Phage–Host Interaction
Host-range matrix design and heatmap reporting template
Efficiency of plating (EOP) computation and uncertainty model
Receptor-binding protein variant analysis across hosts
Adsorption assay workflow and rate constant estimation
CRISPR spacer matching to infer historical host associations
Restriction-modification motif analysis and evasion hypotheses
Anti-CRISPR catalog integration for host immunity context
Host defense gene profiling from host genomes (optional)
Phage receptor prediction from tail fiber domains
Surface polysaccharide locus association with susceptibility
Co-evolution signal detection using mutation enrichment
Transcriptomic response analysis plan for infected hosts (optional)
Phage fitness modeling across environmental conditions
Host growth curve normalization for infection experiments
Phage inhibition zone measurement and QC rubric
Phage depolymerase domain screening and functional hints
Cross-resistance mapping for phage cocktails
Host-range generalist vs specialist classification metrics
Host–phage interaction network analysis and centrality measures
Publication-ready interaction summary tables and figures
Phage Therapy, AMR & Safety Screening
Lytic vs temperate lifestyle prediction with evidence tiers
Integrase and repressor screening to flag lysogeny risk
Toxin and virulence factor screening with curated catalogs
AMR gene screening and phenotype risk interpretation
Genome completeness and contamination gates for therapy use
Candidate scorecard design: QC, safety, and efficacy signals
Phage cocktail design using complementarity and coverage metrics
Synergy testing plan with antibiotics and dosing matrices
Biofilm disruption assay analytics and reporting template
Endotoxin and impurity documentation checklist (research use)
Resistance emergence modeling across serial passage experiments
Phage–antibiotic antagonism detection and mitigation plan
Stability and shelf-life data model for candidate phages
Regulatory-style documentation outline for research prototypes
Risk assessment template for genome-encoded cargo genes
Host range and safety trade-off optimization framework
Manuscript-ready therapy candidate comparison tables
Genotype–phenotype concordance checks for safety calls
Ethics and data governance notes for clinical metadata
Publication pack: SOPs, figures, code, and limitations
Virome Metagenomics & Environmental Phageomics
Metavirome read QC and host contamination filtering workflow
Assembly and binning strategy for viral metagenomes
Viral contig identification using marker and k-mer methods
Read-based abundance estimation and normalization choices
Alpha and beta diversity metrics for phage communities
Seasonality analysis of environmental phage populations
Phage population dynamics modeling using time-series data
Viral-host linkage inference using CRISPR spacers and tethers
Auxiliary metabolic gene profiling in viromes
Network analysis of shared genes across virome contigs
Benchmarking contig quality with completeness estimates
Environmental metadata integration and multivariate models
Source tracking of phage signatures across sites
Functional shift analysis across pollution or nutrient gradients
Rarefaction and sampling depth sufficiency checks
Visualization pack: Sankey, ordination, and network plots
Detection of jumbo phage contigs and annotation plan
Prophage signal filtering to focus on free virions
Re-analysis of public virome datasets with updated tools
Reproducible metagenomics pipeline with containerization
Evolution, Recombination & Population Genomics
Recombination breakpoint detection across phage lineages
Selective sweep detection using within-lineage variants
Population structure inference using SNP and gene content
Mutation spectrum analysis and context biases
Modular evolution analysis of structural and replication genes
Gene gain-loss modeling across a phage clade
Phage core genome definition and stability checks
Phage pangenome openness estimation and interpretation
Co-phylogeny analysis of hosts and phages with permutations
Adaptive evolution tests on receptor-binding proteins
Effective population size proxy estimation from diversity
Phylogeography mapping using sample location metadata
Temporal signal assessment for dated sampling series
Within-sample microdiversity and quasispecies reporting
Transmission cluster inference for outbreak-linked phages
Convergent evolution scan across independent isolates
Accessory gene hotspots and their ecological correlates
Evolutionary rate comparison across environments
Simulation study to validate inference thresholds
Publication-ready evolution figure set and methods appendix
Structural Biology, Proteins & Systems
Capsid and tail protein family clustering and annotation
Structural prediction workflow using modern protein models
Domain architecture comparison for tail fibers and spikes
Packaging ATPase motif analysis and functional inference
Terminase large subunit phylogeny for packaging types
Portal protein conservation analysis across families
Virion proteomics mapping plan and data integration (optional)
Protein–protein interaction hypothesis network for assembly
Structural module boundary detection using synteny and domains
Receptor-binding site motif scan and diversity summaries
Endolysin domain classification and substrate prediction
Holin topology prediction and lysis timing hypotheses
Depolymerase candidate identification for capsule targets
Comparative structural models for vaccine display scaffolds
Quality assessment of predicted structures and confidence plots
Structure-guided mutation shortlist for binding enhancement
Phage display library design outline (research use)
Figure pack: structure cartoons and domain maps
Protein family HMM building for custom phage datasets
Functional systems map linking modules to lifecycle stages
Tools, Databases & Reproducible Informatics
Curated phage genome database schema with versioning
FASTA and GFF validation toolchain and unit tests
Automated metadata linter for phage submissions
Web-ready genome browser track generation workflow
Interactive dashboards for QC and annotation summaries
Standard operating procedure for reproducible notebooks
Containerized pipeline build with pinned tool versions
Workflow orchestration using Snakemake or Nextflow
Benchmark datasets and golden outputs for regression testing
API design for querying phage features and host range
Searchable gene catalog with orthogroup links
Provenance tracking: parameters, hashes, and run logs
Documentation pack: readme templates and citation files
Manuscript figure automation with consistent styling
Data sharing checklist aligned to repository requirements
License and attribution compliance for reference databases
Compute cost estimation for large-scale phage analyses
Error handling and retry rules for batch processing
Quality gate report card for each project run
Final deliverable bundle checklist for publication
Contact Us