Whole Genome Sequencing Applications

Whole Genome Sequencing (WGS) has enabled comprehensive decoding of the sequence of entire genomes of organisms. Such information is crucial for understanding functional and evolutionary history of organisms,as well as to identify mutations and genetic variations that are responsible for causing genetic disorders,development of cancer, disease outbreaks, evolution of strains with novel pathogenic traits, etc. At Hi-Gx360 ®, we use a read-to-annotation approach to generate in detail all the information needed to understand functions of all predicted genes present in the organism. Assembled genomes may not be 100% complete, hence, further gap-filling can be achieved using one of many long read sequencing technologies.

• Sequence close relatives of reference-organisms or entirely novel organisms (de-novo)
• Obtain high-resolution and accurate genomic characterization using 2 x 150 or 2 x 300 bp reads
• Data supplied with interactive QC report.
• Predesigned identification service under Isolate-to-Identity covering all organisms
• Receive raw sequence reads, assembled contigs & scaffolds Along with bioinformatics analysis customised to fit your needs
• Choose from basic or advanced bioinformatics.

Recommendations

Deliverables

• Run information, Statistics of raw data & FASTQ files
• Reference Genome Mapping files/ De-novo Genome Mapping files, Functional Annotations, Gene predictions,Gene annotations, Pangenome analysis
• Advanced analysis customized to your project needs

Whole Exome Sequencing Applications

The human genome has 180,000 coding regions which account for 1.7% of the genome. An estimated 85% of human diseases with genetic basis occur due to aberrations in these coding regions. Targeted sequencing of these regions of the genome are termed as whole exome sequencing (WES). Exome sequencing is a more cost-effective option than sequencing the whole human genome.

This sequencing method uses a targeted capture approach where biotinylated probes are deployed against the coding regions of the fragmented human genome to capture and pull down these parts with streptavidin coated beads. The fragments thus obtained are sequenced on the NextSeq™ 550 platform. This strategy results in a 100-fold increase in coverage of the relevant sections of the genome.

• Lower cost and wide availability
• Sequencing coverage on target upto 30X
• Detection of coding single-nucleotide polymorphism (SNP) variants as sensitive as whole genome sequencing
• A smaller data set for faster and easier analysis compared to whole genome sequencing
• Standard sequencing coverage ≥ 50X; cancer sample ≥ 100X. More SNPs can be gained by increasing the coverage.
• Cost-effective library preparation and exome enrichment solutions

Exome Sequencing Recommendations

Deliverables

• Run information, Statistics of raw data & FASTQ/VCF files
• Mapping statistics, Statistics of sequencing reads
• SNPs and InDels calling, Variant annotation, SNVs concordance, Tumor-Normal paired analysis

Amplicon-based microbiome sequencing Applications

• A potential tool for high-throughput phylogenetic analysis of microbial communities.
• Based on phylogenetic marker genes; 16S, 18S rRNA genes & ITS region
• Allows species identification and taxonomic diversity characterization
• Provides detail insight of genus and species

Advantages of amplicon-based phylogenetic gene marker sequencing

• Marker genes are omnipresent
• Marker genes are highly abundant to those of other genes
• Measures phylogenetic relationships across different taxa
• Easily estimate relative abundance of microbial communities
• Highly cost-effective

Recommendations

Deliverables

• Run information, Statistics of raw data & FASTQ files
• Taxonomic profiles, Functional Annotations, Metagenome assembled genomes (MAGs)
• Advanced analysis customized to your project need

Shotgun-based Metagenome Sequencing Applications

Shotgun metagenomics is a proven tool to study environmental, agricultural & human microbiomes, pathogen identification & surveillance as well as monitoring of anti-microbial resistance genes in the environment. Some of the most common applications include:

• Identification and classification of microbial communities
• Novel biomarker discoveries
• De-novo assembly & characterizations of novel genomes
• Discovery of novel enzymes and metabolic pathways
• Relative abundance analysis of microbial communities

Recommendations

Deliverables

• Run information, Statistics of raw data & FASTQ files
• Taxonomic profiles, Functional Annotations, Metagenome assembled genomes (MAGs)
• Advanced analysis customized to your project need

Transcriptomics

RNA sequencing (RNA-seq) is a powerful and widely used technique for transcriptome analysis that has revolutionized the field of molecular biology. It allows researchers to study gene expression at an unprecedented level of detail, providing valuable insights into the mechanisms of cellular processes and disease pathogenesis. RNA-seq works by converting RNA molecules into a library of cDNA fragments that are then sequenced using high-throughput sequencing technologies.

• Identify and quantify gene expression levels, detect novel transcripts & investigate alternative splicing patterns
• Detect post-transcriptional modifications such as RNA editing
• Wide dynamic range and low input requirements
• Work with a variety of sample types, from single cells to complex tissues.
• Integrate with other types of omics data to obtain a more comprehensive view of biological systems.

Ready-to-load / Custom NGS Services

• User supplies ready-to-run library pool and is responsible for data quality, read distribution or failure due to user errors.
• Sequencing using relevant PE read chemistry to generate data.
• Sequencing Run information.
• Raw data information (number of quality reads generated including average Q score), adaptor trimmed and clipped reads as fastQ files.

Custom Sequencing

Supplemental Services

Only offered in combination with other NGS service codes, NOT separately