Project Examples

Here are some examples of Bioinformatic analyses we have expertise in conducting. 

We have experience working with many diverse data and organism types, so even if your topic is not listed in our project examples, we are likely to be able to assist you.

Deliverables for Basic/Standard Analysis

MAX Turnaround time – 2 months depending on application and sample size

 

1. Whole Genome Sequencing

Prokaryotes

  • RE-SEQUENCING: Raw Data QC and Report, Alignment Statistics and Report, Variation Calling Report (SNP, InDels), Gene Annotation Table with Variations.
  • DENOVO: Raw Data QC and Report, Assembly Statistics and Report, Genome Finishing using Closest homolog, rRNA identification and analysis report, Phage Identification and analysis report, Plasmid Identification, and analysis report, RAST Annotation.

Eukaryotes

  • RE-SEQUENCING/TARGETED/EXOME: Raw Data QC and Report, Alignment Report, Variation calling Report (SNP, InDels), Basic Variation Annotation, and Effect Analysis Report.
  • DENOVO: Raw Data QC and Report, Assembly Statistics and Report, Gene Prediction and Annotation Report. Data generation depends on predicted genome size

2. Transcriptome Sequencing

Prokaryotes

  • RE-SEQUENCING: Ribo Depletion (rRNA Depletion) – Raw Data QC and Report, Read Alignment to reference genome and transcript Identification, Comprehensive Transcript Annotation, Functional Classification of Annotated Transcript, Expression Profiling, Quantification & Expression Profiling of transcripts, Differential Analysis among the conditions, Biological Significance Analysis of differentials.

Eukaryotes

  • RE-SEQUENCING: – Raw Data QC and Report, Read Alignment to reference genome and transcript Identification, Quantification & Expression Profiling of transcripts, Differential, Analysis among the conditions, Biological Significance Analysis of differentials (n-1). All pictorial representations of comparisons will be according to n-1
  • DENOVO: Raw Data QC and Report, De novo assembly, Assembly Evaluation & Filtering, Sequence homology-based Transcript Annotation using Blast2Go – REFSEQ, Expression Profiling, Differential Analysis among the conditions, Biological Significance Analysis of differentials (n-1). ALL pictorial representation LL of comparisons will be according to n-1.

3. Chip Sequencing

Raw Data QC and Report, Alignment Report, Peak Identification, and Enrichment Report, Peak Annotation Report

5. SmallRNA Sequencing

Sample wise Raw Data QC, Unique tags and abundance Report, Known Small RNA analysis report, Identification and Quantitation of Known miRNAs, Expression Profiling and Differential Expression Analysis of Known miRNAs.

4. Metagenome Sequencing

Sample Grouping or individual as per experimental design, Group-wise OTU Clustering and abundance Report, OTU identification and taxonomic annotation Report (Sample Wise – Genius Level) and OTU Fasta file will be provided, Pie chart representation TOP 10 taxonomic classification; phylum to species-level.

6. Microbiome Sequencing

Pre-processing of reads including Quality Filtering, trimming low-quality reads, De-Replication, Sequence reconstruction and grouping, Gene prediction, Functional Annotation.

Deliverables for Advanced Analysis

MAX TAT – 6 months depending on the project requirement and sample size

 

1. Whole Genome Sequencing

Prokaryotes

  • RE-SEQUENCING: Raw Data QC and Report, Alignment Statistics and Report, Variation Calling Report (SNP, InDels), Gene Annotation Table with Variations, Structural Variations (Inversion, Deletion, Insertion, Translocation, Transversion) analysis report, Comparative Genome analysis – Across selected genomes, High SNP and Low SNP Region, Generic and NonGeneic SNPs, SNP Density Analysis, Synonymous and Non-synonymous SNPs, Effect of Frameshift Indels on Gene Prediction, Submitting Data to NCBI -SRA, Support in providing write up on methods for the manuscript purpose (Time Limit: 3-6 month)
  • DENOVO: Raw Data QC and Report, Assembly Statistics and Report, Genome Finishing using Closest homolog, rRNA identification and analysis report, Phage Identification and analysis report, Plasmid Identification and analysis report, Phylogeny 16s RNA based, COG Analysis, Interproscan Analysis, AAI and ANI analysis with the selected reference genome, Antibiotic resistance gene analysis with reference to transposable elements, PAN and Core genome analysis, Synteny Analysis, Chromosome Mapping, Plasmid Re-construction from whole-genome, Submitting Data to NCBI- SRA, Support in providing write up on methods for the manuscript purpose (Time Limit: 3-6 month)

Eukaryotes

  • RE-SEQUENCING/TARGETED/EXOME: Raw Data QC and Report, Alignment Report, Variation calling Report (SNP, InDels), Basic Variation Annotation and Effect Analysis Report, All the deliverables from Standard Analysis, Structural Variation Analysis Report, Variation Effect Analysis Report, Pathway and GO analysis of variations, Copy Number Variation Analysis, Data Submission to NCBI, Comparative Exome Analysis, Submitting Data to NCBI- SRA, Support in providing write up on methods for the manuscript purpose.
  • DENOVO: Raw Data QC and Report, Assembly Statistics and Report, Gene Prediction and Annotation Report, Prediction of rRNAs, tRNAs, Repeat Analysis, Identification of Transposons, Domain Identification, Analysis of Virulence genes, Analysis of CaZymes, Synteny Analysis, Comparative Exome Analysis, Submitting Data to NCBI- SRA, Support in providing write up on methods for the manuscript purpose.

2. Transcriptome Sequencing

Prokaryotes

  • RE-SEQUENCING: Ribo Depletion (rRNA Depletion) – Raw Data QC and Report, Read Alignment to reference genome and transcript Identification, Comprehensive Transcript Annotation, Functional Classification of Annotated Transcript, Expression Profiling, Quantification & Expression Profiling of transcripts, Differential Analysis among the conditions, Biological Significance Analysis of differentials, Inter and Intra Gene List Comparisons, Gene and Pathway enrichment analysis, GO and Pathways based Gene Regulatory Network Modelling, Submitting Data to NCBI- SRA, Support in providing write up on methods for the manuscript purpose.

Eukaryotes

  • RE-SEQUENCING:  Raw Data QC and Report, Read Alignment to reference genome and transcript Identification, Expression Profiling, Quantification & Expression Profiling of transcripts, Differential Analysis among the conditions, Biological Significance Analysis of differentials, Inter and Intra Gene List Comparisons, Gene and Pathway enrichment analysis, GO and Pathways based Gene Regulatory Network Modeling, Functional classification of expressed transcripts Submitting,  Data to NCBI-SRA, Support in providing write up on methods for the manuscript purpose. 
  • DENOVO: Raw Data QC and Report, De novo assembly, Assembly Evaluation & Filtering, Sequence homology-based Transcript Annotation using Blast2Go – NRDB, Expression Profiling, Differential Analysis among the conditions, Biological Significance Analysis of differentials, Sequence homology-based Transcript  Annotation against the customized database, Inter and Intra Gene List Comparisons, Gene and Pathway enrichment analysis, Functional Classification of Annotated Transcript, GO and Pathways based Gene Regulatory Network Modeling, Data to NCBI-SRA, Support in providing write up on methods for the manuscript purpose.

3. Chip Sequencing

Raw Data QC and Report, Alignment Report, Peak Identification, and Enrichment Report, Peak Annotation Report, Motif Identification, Statistical analysis of Peak Reproducibility (If replicates are provided), Significant GO and Pathway Analysis, Data to NCBI-SRA, Support in providing write up on methods for the manuscript purpose.

5. SmallRNA Sequencing

Raw Data QC and Report, Known Small RNA analysis report, Identification and Quantitation of Known miRNAs, Expression Profiling and Differential Expression Analysis of Known miRNAs, Novel miRNA Identification (In case of reference genome availability) and analysis report, Characterization of other small RNAs like siRNA, piRNA, snoRNA, miRNA Target Prediction / Identification, Significant GO and Pathway Analysis of targets of differentially expressed miRNAs, DData to NCBI-SRA, Support in providing write up on methods for the manuscript purpose.

4. Metagenome Sequencing

Sample Grouping/Individual (either one) as per experimental design, Group-wise OTU Clustering and abundance Report, OTU identification and taxonomic annotation Report (Sample Wise – Genius Level) and OTU Fasta file will be provided, Pie chart representation TOP 10 taxonomic classification (Phylum to Species-level), Differential Metagenome based on sample conditions, Diversity Analysis (Alpha and Beta), Rarefaction Curves, PCoA Plot (required minimum six samples), Krona Plot at the genus level, Heat-Maps for comparisons, Species-level annotation (If V3 & V4 is covered), Data to NCBI-SRA, Support in providing write up on methods for the manuscript purpose.

6. Microbiome Sequencing

Pre-processing of reads including Quality Filtering, Trimming low quality reads, De-Replication, Sequence reconstruction and grouping, Gene and regulatory element prediction, Functional Annotation, Differential Microbiome based on sample parameters, Statistical analysis of Microbiome based on OTUs, Diversity Analysis (Alpha and Beta), Rarefaction Curves, Species-level annotation, Seed Subsystem classification, COG, KEGG Analysis, Gene Ontology and Pathway Analysis (Functional Microbiome Analysis), Data to NCBI-SRA, Support in providing write up on methods for the manuscript purpose.