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 analysing the human genome. Researchers use large whole-genome sequencing to analyse tumours, 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
De novo Assembly
Summarized Genome Assembly Statistics
Estimation of Genome Size
Final assembled genome sequence (contigs / scaffolds) in fasta file format
Reference genome based analysis
Mapping of high quality reads on reference genome
Alignment report summarizing mapping results
Functional annotation of gene
Gene prediction
Comprehensive compiled report and data
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
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 labour-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
De novo Assembly
Summarized Genome Assembly Statistics
Estimation of Genome Size
Final assembled genome sequence (contigs / scaffolds) in fasta file format
Reference genome based analysis
Mapping of high quality reads on reference genome
Alignment report summarizing mapping results
Functional annotation of gene
Gene prediction
Comprehensive compiled report and data
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 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 analyses 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 analysed as per quotation.
TAT – Turn Around Time 4-5 weeks
TAT may vary for large order
Whole Metagenomics
NGS based Service
Whole Metagenomics :
The whole metagenome sequencing analysis generally includes sequencing of the complete metagenome samples followed by de novo assembly of multiple genomes from sequence reads of multiple species in an environmental sample. During assembly the paired end reads are compared to each other, and then overlapped reads are used to build longer contiguous sequences are further analysed for prediction of genes and functional annotations.
Process:
- Preparation of DNA sequencing library, 2×150 PE Hiseq sequencing to generate 25-30 million reads (R1+R2) per sample.
- Sequence data QC and quality based filtering of k-mer based microbial identification using NCBI nt database, metagenome assembly, gene prediction, taxonomical identification, functional annotation (COG and KO), results visualization using pie charts, Ssnaky plots.
Sample Requirements :
200ng of the DNA sample; Concentration: 10ng/ µl; For analysis: upto 20 GB data
Deliverables:
Data will be shared on Cloud.
Fastq files (raw reads), QC data; Project Report; Data analysed as per quotation.
TAT – Turn Around Time 8-12 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 :
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Identifies variants across a wide range of applications
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Achieves comprehensive coverage of coding regions
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Provides a cost-effective alternative to whole-genome sequencing (4–5 Gb of sequencing per exome compared to ~90 Gb per whole human genome)
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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 DNA or 5 µg of purified DNA; Concentration: 200ng/ µl
Standard analysis specifications :
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Histogram of depth distribution in target region
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Sequencing library preparation
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Exome enrichment
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Mapping statistics
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Alignment of QC filtered sequence data onto the reference genome, variant calling (SNVs and small InDels) and variant annotation
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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.
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TAT – Turn Around Time 4-5 weeks
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TAT may vary for large order
Sequence based Genotyping
NGS based Service
Sequence based Genotyping:
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 analysed 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 analyse 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, analyse 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 analysed as per quotation; Detailed Project report