GREENGATE GENOMICS
SERVICES
GREENGATE GENOMICS
DNA based services
AMPLICON DATA BASED SERVICES
- Barcode primer check
- Library preparation
- Arrange sequencing
- Demultiplexing samples
- Quality control, decontamination and chimera filtering
- Taxonomic assignment
- Community data (in OTU or ASV format)
- Krona plot
- Functional prediction based on 16S rRNA gene data
METAGENOMIC SERVICES FOR NANOPORE LONG READ DATA
- Library preparation prior to sequencing
- Sequencing
- Effective raw reads calling with powerful GPU
- Quality control on sequencing data
- Assembly and gene calling
- Genomic binning to MAGs
- Taxonomic and functional annotation
- Pathway analysis
- Phylogenetic tree of MAGs
We offer selected Oxford Nanopore sequencing services. Please visit our Nanopore Sequencing Service overview page for more details.
METAGENOMIC SERVICES FOR ILLUMINA SHORT READ DATA
- Raw data (paired-end or single-end) quality check
- Decontamination
- Assembly short reads to contigs (long reads)
- Gene calling, quantification from contigs
- Quality control, decontamination and chimera filtering
- Genomic binning (Metagenome-Assembled Genomes, MAGs) and taxonomic assignment
- Functional annotation for genes on contigs or MAGs
- Pathway analysis based on contigs or MAGs
- Phylogenetic tree of MAGs
GREENGATE GENOMICS
RNA based services
METATRANSCRIPTOMIC ANALYSIS SERVICES (Illumina)
- Raw data (paired-end or single-end) quality check
- Assembly and gene calling
- Functional and taxonomic annotation of genes
- Differential gene expression
GREENGATE GENOMICS
downstream analysis
BIOSTATISTICS
- Network analysis (dissimilarity- or correlation-based)
- Module/cluster identification from network
- PERMANOVA (e.g. adonis, db-RDA)
- Mantel test
- LEfSe (Liner discriminant analysis effect size) differential abundance analysis
- Structural equation modelling (Path analysis, confirmative factor analysis)
- Rarefaction and rank abundance curve
- Alpha diversity and beta diversity
- Indicator species
- Generalist and specialist species
- Dissimilarity measure calculations (e.g. Bray-Curtis, Euclidian, Jaccard distance)
- Correlation with environmental and chemical measurements
DATA VISUALIZATION
- Custom figures (e.g. bubble plot, heatmap, Venn diagram, Chord diagram, Sankey or custom advance plots)
- Phylogenetic Trees
- Ordination Graphs (PCA, PCoA, NMDS, CCA)
GREENGATE GENOMICS
ACCESSORY services
CONSULTATION SERVICES
- Consultation on experiment design
- Data analysis strategy
- Recommendation of right sequencing platform suitable to answer your question
- Quotation of service
WORKSHOP AND TRAININGS
- Tool specific training
- Installation and usage troubleshooting
- Rent a Bioinformatician - personal bioinformatic guidance
DATA & OTHER SERVICES
- Raw data download from your service company
- Data submission to Archive database (e.g. SRA, ENA, DDBJ)
- Raw data storage on local machine
- Reference database for specific genes, proteins or taxonomic groups
- Manuscript assistant in bioinformatics and statistics
- Cooperation (e.g. bioinformatic partner) in funding application
GREENGATE GENOMICS
PIPELINE DEVELOPMENT
PIPELINE DEVELOPMENT
- Custom bioinformatic pipeline for your data
- Data analysis script based on your needs
