Name of Service | Service Description | Product No. |
Whole Genome Re-sequencing *For human, animal, plant, fungi, bacterium, virus, or insect | - Sequence QC
- Mapping onto reference genome; statistics of sequencing depth and coverage
- Variant (SNP & InDel) calling, annotation and statistics
| NGS-0100 Series |
De novo Whole Genome Sequencing *For fungi, bacterium, or virus | - Sequence QC
- De novo assembly for genome size <10Mb
- Gene Prediction
| NGS-0200 Series |
Low Coverage Whole Genome Sequencing *For animal, plant, or insect | - Sequence QC
- Tabulation of variants in vcf table
- Tabulation of Phylogeny
| NGS-0300 Series |
Whole Exome Sequencing *For human or mouse | - Sequence QC
- Mapping onto reference genome; statistics of sequencing depth and coverage
- Variant (SNP & InDel) calling, annotation and statistics
- Somatic variant (SNP, InDel or CNV) calling, annotation and statistics (paired tumor samples)
| NGS-0400 Series |
Transcriptome Re-sequencing *For mRNA, small RNA or lnRNA | - Sequence QC
- Mapping Reads to Reference Genome (provided by customer)
- Gene Expression Quantification
- Correlation analysis (For biological replicates only)
- Differential Expression Analysis (two or more groups of samples)
- GO Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
- KEGG Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
| NGS-0500 Series |
De novo Transcriptome Sequencing *For mRNA only | - Sequence QC
- De novo Transcriptome Assembly
- Gene Functional Annotation Using different databases (e.g. NR, NT, KO, Swiss-Prot, GO and/or PFAM)
- GO, COG, KEGG Classification
- CDS Prediction
- Gene Expression Analysis
- Correlation analysis (For biological replicates only)
- Differential Expression Analysis (two or more groups of samples)
- GO Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
- KEGG Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
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Shotgun Metagenomics Sequencing *For environmental DNA | - Sequence QC
- Filtering host genome sequences
- Assembly
- Species annotation (microorganic sequences extracted from NCBI NR database)
- Gene prediction
- Gene annotation (KEGG, eggNOG, CAZy database)
- Species/Gene/Function abundance statistics and cluster analysis
- Comparative analysis (among samples)
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Amplicon Sequencing (16s/18s/ITS) – OTU Clustering *For bacterial 16s region (v1-v3, v4, v3-v4, v4-v5, v4-v6 or v7-v9) *For archaeal 16s region (v4, v3-v5 or v3-v6) *For eukaryotic 18s region (v4 or v9) *For fungal ITS region (ITS1 or ITS2)Note1: Underlined = popular region. Note2: If you have any target taxonomy in the standard analysis, the selection of the specific region must refer to the existing literature review. | - Sequence QC
- OTUs (Operational Taxonomic Units) Clustering and Filtering
- OTUs Analysis and Species Annotation, including KRONA results, OTUs Heatmap, Taxonomic Abundance and up to 5 Venn diagrams
- Alpha-diversity Analysis, including Alpha Indices table with ANOVA, Rarefaction curve, Rank abundance curve
- Beta-diversity Analysis, including Ordination (CCA, RDA, DPCoA, NMDS, MDS, PCoA), Unifrac distance analysis, UPGMA (Unweighted Pair-group Method with Arithmetic Means)
- Phylogenetic Trees, including OTU co-occurrence networks & Metacoder
- Statistics Between Groups: DESeq2, ANOSIM, LEfSE
- Metagenome Functional Prediction using Picrust2
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Amplicon Sequencing (16s/18s/ITS) - DADA2 | - Data QC and trimming
- Amplicon Sequence Variants (ASV) table
- Taxonomic characterization
- Alpha diversity analysis
- Beta diversity analysis
- Phylogenetic tree
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Metabarcoding Sequencing *For any custom gene used for DNA barcoding | - Sequence QC
- OTUs (Operational Taxonomic Units) Clustering and Filtering
- Species Annotation by comparing unique sequences against a curated reference database from NCBI
- OTU Analysis, including KRONA results, OTUs Heatmap, Taxonomic Abundance and up to 5 Venn diagrams*.
- Alpha-diversity Analysis, including Alpha Indices table with ANOVA, Rarefaction curve, Rank abundance curve.
- Beta-diversity Analysis, including Ordination (CCA, RDA, PCoA, NMDS, MDS) and PCoA Plots.
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Whole Genome Bisulfite Sequencing (WGBS) *For human only | - Sequence QC
- mCs detection, methylation level calculation
- Methylation level and frequency distribution
- Differentially Methylated Site (DMS) detection
- Differentially Methylated Regions (DMRs), Differentially Methylated Promoter (DMPs) detection and annotation
- Function enrichment of DMR-associated genes and DMP-associated genes
- Visualization of BS seq data
- Comparative analysis (among samples)
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ChIP (Chromatin Immuno Precipitation) Sequencing *For any organism with suitable reference genome available | - Sequence QC
- Mapping onto reference genome
- Peak calling
- Motif prediction
- Peak annotation and functional analysis of peak-associated genes
- Summary of differential peaks and functional analysis of differential peak related genes
- Visualization of ChIP-seq data
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