At 1st BASE, we offer an assortment of standard to personalised bioinformatics options to translate these data into useful information that is critical to complete the picture.

For Standard Bioinformatics Analysis, you may request demo report before committing the project. Should you need custom analysis to be conducted, please feel free to contacts us.

All project information and data are kept confidential. Non-disclosure agreement is available upon request. All sequencing raw data and analysed data have the delivery options of either downloading through our secure servers (Cloud or Web Services) or through Illumina BaseSpace account. We are also able to send the NGS data in flash drive or external hard disk to you if you have concern about your internet download speed.

Standard Bioinformatics Analysis

Name of ServiceService DescriptionProduct 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)
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)
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
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
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.
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)
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

 

Custom Bioinformatics Analysis

Name of ServiceService DescriptionProduct No.
Customized Analysis Hybrid WGS Bacterium
    • Data trimming to pick out the best reads comprising 40X coverage
    • Assemble the reads into long contigs, polish the assembly using the PacBio reads
    • Error correction with Illumina clean reads
    • Annotate the assembled genome with open reading frames
    • Assembly of Plasmids
NGS-0108
Customized Analysis Hybrid WGS Fungi
    • Data trimming to pick out the best reads comprising 40X coverage
    • Assemble the reads into long contigs, polish the assembly using the PacBio reads
    • Error correction with Illumina clean reads
    • Annotate the assembled genome with open reading frames 
NGS-0109
Customized Analysis for Data Integration (DNA and RNA)
    • Data intergration from whole genome sequencing (hybrid assembly of Pacbio long reads and Illumina short reads) and (no.) sets of Transcriptomic data (6Gb/12Gb each)
    • Assemble the reads into long contigs with RNA evidences
    • Annotate the assembled genome with open reading frames
    • Deliverables in fna and gtf format
NGS-0112

 

For others, please enquire.

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Sample Submission Guidelines for gDNA/RNA Extraction Projects