NGS Based Services

Better options, better outcomes

Robust analysis for the data insights you need. Complete sample-to-analysis solutions including customizable extraction and data analysis options available. We offer both standard and custom services for extraction, library preparation, sequencing, and bioinformatics.

NGS provides researchers the capability to profile (16S rRNA/18s/ITS based) entire microbial communities from complex samples, discover new organisms and explore the dynamic nature of microbial population under changing conditions. 

 

Metagenomics

NGS based Service

Metagenomics :

Unlike capillary sequencing (Sanger) or PCR-based approaches, next-generation sequencing (NGS) is a culture-free method that enables analysis of the entire microbial community within a sample. With the ability to combine many samples in a sequencing run, microbiology researchers can use NGS-based 16S/18S/ITS amplicon sequencing a cost-effective technique to identify strains that may be difficult to find using other methods.

Sample Requirement :

Sufficient sample to isolate 5 µg of genomic DNA or  5 µg of purified genomic DNA  with 260 / 280 ratio of  1.8 – 1.9; Concentration of 200ng/ µl.

Standard analysis specifications :

  • Metagenome analysis for OUT assignment

  • Abundance (Alpha diversity)

  • Beta diversity analysis

  • Data visualization (rarefaction curve, stacked bar plots, heatmaps, PCOA plots)

*Custom specification can be made based on client’s preference

Coverage :  0.1million reads/sample

Deliverables : 

Data will be shared on cloud.

Fastq Files (raw reads), QC data; Project Report; Data analysed as per quotation.

  • TAT – Turn Around Time 4-5 weeks

  • TAT may vary for large order

Whole Genome Sequencing

NGS based Service

Whole Genome Sequencing :

Large Whole Genome Sequencing:

Whole-genome sequencing is the most comprehensive method for analyzing the human genome. Researchers use large whole-genome sequencing to analyze tumors, investigate causes of diseases, select plants and animals for agricultural breeding programs and identify common genetic variations among populations.

Sample Requirement :

Sufficient sample to isolate 5 µg of DNA or 5 µg of purified genomic DNA; Concentration: 200ng/ µl.

Standard analysis specifications :

De novo genome based analysis    

  1. De novo Assembly

  2. Summarized Genome Assembly Statistics

  3. Estimation of Genome Size

  4. Final assembled genome sequence (contigs / scaffolds) in fasta file format

Reference genome based analysis 

  1. Mapping of high quality reads on reference genome

  2. Alignment report summarizing mapping results

  3. Functional annotation of gene

  4. Gene prediction

  5. Comprehensive compiled report and data

Deliverables: 

Data will be shared on Cloud.
Fastq files (raw reads), QC data; Project Report; Data analyzed as per quotation.

  • TAT – Turn Around Time 4-5 weeks

  • TAT may vary for large order

Small Whole Genome Sequencing:

While whole-genome sequencing is commonly associated with sequencing human genomes, the scalable, flexible nature of next-generation sequencing (NGS) technology makes it equally useful for sequencing any microbial species such as agriculturally important live-stocks, plants or disease-related microbes. NGS-based “small” whole-genome sequencing (WGS) allows microbiology researchers to sequence hundreds of prokaryotic organisms with the power of multiplexing. Unlike traditional methods, no labor-intensive cloning steps are required. 

Sample Requirement :

Sufficient sample to isolate 5 µg of DNA or 5 µg of purified genomic DNA; Concentration: 200ng/ µl.

Standard analysis specifications :

De novo genome based analysis    

  1. De novo Assembly

  2. Summarized Genome Assembly Statistics

  3. Estimation of Genome Size

  4. Final assembled genome sequence (contigs / scaffolds) in fasta file format

Reference genome based analysis 

  1. Mapping of high quality reads on reference genome

  2. Alignment report summarizing mapping results

  3. Functional annotation of gene

  4. Gene prediction

  5. Comprehensive compiled report and data

Deliverables: 

Data will be shared on Cloud.
Fastq files (raw reads), QC data; Project Report; Data analyzed as per quotation.

  • TAT – Turn Around Time 4-5 weeks

  • TAT may vary for large order

 

Whole Exome Sequencing

NGS based Service

Whole exome sequencing:

The most widely used targeted sequencing method is exome sequencing. The exome (the protein-coding regions of the human genome) represents less than 2% of the genome but contains ~85% of known disease-related variants making whole-exome sequencing a cost-effective alternative to whole-genome sequencing.

Exome sequencing can efficiently identify coding variants across a wide range of applications including population genetics, genetic disorders and cancer studies.

Advantages :

  • Identifies variants across a wide range of applications

  • Achieves comprehensive coverage of coding regions

  • Provides a cost-effective alternative to whole-genome sequencing (4–5 Gb of sequencing per exome compared to ~90 Gb per whole human genome)

  • Produces a smaller, more manageable data set for faster, easier analysis compared to whole-genome approaches

Sample Requirement :

Sufficient sample to isolate 5 µg of RNA or 5 µg of purified RNA; Concentration: 200ng/ µl

Standard analysis specifications :

  • Histogram of depth distribution in target region

  • Sequencing library preparation

  • Exome enrichment

  • Mapping statistics

  • Alignment of QC filtered sequence data onto the reference genome, variant calling (SNVs and small InDels) and variant annotation 

  • Comprehensive compiled report and data

Coverage: 100X

Deliverables: 

Data will be shared on cloud.

Fastq Files (raw reads), QC data; Project Report; Data analysed as per quotation.

  • TAT – Turn Around Time 4-5 weeks

  • TAT may vary for large order

Sequence based Genotyping

NGS based Service

Sequence based Geotyping:

Genotyping by Next-Generation Sequencing is a genetic screening method for discovering novel plant and animal SNPs and performing genotyping studies. For some applications, such as genotype screening and genetic mapping, sequence-based genotyping provides a low-cost alternative to arrays for studying genetic variations (SNPs). 

Genotyping by sequencing is cost-effective for populations with complex genomes or limited available resources. Advantages are:

  • Sequences predetermined areas of genetic variation over many samples

  • Provides a low cost per sample for certain applications

  • Reduces ascertainment bias compared to arrays

  • Identifies variants other than SNPs, including small insertions, deletions and microsatellites

  • Enables comparative analyses across samples in the absence of a reference genome

  •  Informs genetic mapping, screening backcross lines, purity testing, constructing haplotype maps, association mapping, and genomic selection for plant studies

Sample requirement:
Sufficient sample to isolate 5 µg of DNA or 5 µg of purified DNA; Concentration: 200ng/ µl

Standard analysis specifications:

  • Data filtering

  • Mapping statistics

  • Variant calling and genotyping

Coverage: 3X-10X

Deliverables:

 Data will be delivered in Pen drive/CD or shared on Cloud.
Fastq files (raw reads), QC data and Project report delivered.
Data analyzed as indicated in quotation.

Small/Micro RNA Sequencing

Small/Micro RNA sequencing :

With NGS-based small RNA-Seq you can discover novel miRNAs and other small non-coding RNAs and examine the differential expression of all small RNAs within a sample. You can characterize variations such as isomers within up to single-base resolution, as well as analyze any small RNA or miRNA without known prior sequence or secondary structure information.

Small non-coding RNAs act in gene silencing and post-transcriptional regulation of gene expression. Small RNA sequencing (RNA-Seq) is a technique to isolate and sequence small RNA species such as microRNA (miRNA). Small RNA-Seq can query thousands of small RNA and miRNA sequences with unprecedented sensitivity and dynamic range.

Sample Requirement :

Sufficient sample to isolate 5 µg of RNA or 5 µg of purified RNA; Concentration: 200ng/ µl

Standard analysis specifications :

  • Data filtering and alignment

  • Adapter clipping

  • Small RNA classification report

  • miRNA identification and quantification

  • miRNA expression profiling report

  • Discovery of novel

    miRNAs

  • Target precision of significant miRNAs and functional analysis based on the target genes

Coverage: 20 million reads

Deliverables : 

Data will be shared on cloud.

Fastq Files (raw reads), QC data; Project Report; Data analysed as per quotation.

  • TAT – Turn Around Time 4-5 weeks

  • TAT may vary for large order

Gene expression profiling by Sequencing

Gene expression profiling by Sequencing :

RNA-Seq solutions provide precise measurement of strand orientation, uniform coverage, and high confidence mapping of alternate transcripts and gene fusions. Discover novel gene isoforms, profile gene expression for select targets of interest, analyze the whole coding transcriptome, and accurately perform transcript abundance and fold-change measurement.

NGS-based RNA sequencing (RNA-Seq) methods can quantify and profile any active gene or transcript, including novel transcripts.
Sample requirement:
Sufficient sample to isolate 5 µg of RNA or 5 µg of RNA; Concentration: 200ng/ µl.
Standard analysis specifications:

  • Data filtering

  • Transcriptome Mapping

  • Gene Expression analysis

Deliverables:

Data will be delivered in Pen drive/CD or shared on cloud
Fastq files (raw reads), QC data; Data analyzed as per quotation; Detailed Project report

 

Whole Transcriptome/ RNA Sequencing

NGS based Service

Whole Transcriptome Sequencing (Eukaryotes) :

Whole-transcriptome analysis with total RNA sequencing (RNA-Seq) detects coding as well as multiple forms of non-coding RNA. Total RNA-Seq can accurately measure gene and transcript abundance and identify known and novel features of the transcriptome.

Total RNA-Seq analyzes both coding and multiple forms of non-coding RNA for a comprehensive view of the transcriptome.

Advantages:

  • Captures both known and novel features

  • Allows researchers to identify biomarkers across the broadest range of transcripts

  • Enables a more comprehensive understanding of phenotypes of interest

  • Allows profiling of the transcriptome across a wide dynamic range

Sample Requirements :

Sufficient sample to isolate 5 µg of RNA or 5 µg of purified RNA; Concentration: 200ng/ µl;

Standard analysis specifications :

Reference genome based analysis 

  • Mapping of high quality reads on reference genome

  • Alignment of report summarizing mapping results

  • Functional annotations of genes

  • Gene prediction

  • Comprehensive compiled report and data

  • Gene annotation and expression (if multiple samples available)

  •  Transcript abundance estimation

  •  Differential gene expression analysis and identification of statistically significant up/down regulated genes

Coverage:10-15  million reads/sample

Deliverables:

Data will be shared on Cloud.

Fastq files (raw reads), QC data; Project Report; Data analyzed as per quotation.

  • TAT – Turn Around Time 4-5 weeks

  • TAT may vary for large order