Long-Read Metagenomics Data Analysis

As a bioinformatics data analysis provider, CD Genomics is experienced in Long-Read Metagenomics Data Analysis and our high-quality data analysis platform will be used to generate high-quality analysis results in a fast analysis cycle.

Introduction

Metagenomics takes the entire microbial community in a specific habitat as a research object, without separating and cultivating, and directly extracts DNA from environmental samples for high-throughput measurement. Metagenome sequencing research eliminated the limitation of pure culture of microorganism isolation, expanded the utilization space of microbial resources, and is effective when studying the environmental microbial communities.

Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way Metagenomics are analyzed. Using Oxford Nanopore Technologies (ONT) and PacBio SMRT technology, we can obtain more genomic information, more accurate species classification, more species identification, and more comprehensive characterization of all aspects of microbial communities, which can restore the information of microbial communities in the environment as realistically as possible, so that we can deeply explore their importance to the whole ecosystem (Bharti & Grimm, 2021).

Application Field

Medical field: the relationship between human microbiome and human health/disease, etc.

Animal: rumen and animal health/nutrient digestion, etc.

Agronomic field: microbial interactions with plants, etc.

Environmental field: haze treatment, sewage treatment, etc.

CD Genomics Data Analysis Pipeline

Bioinformatics Analysis Content

• Data Quality Control
• Assembly
• Metaphlan Species Annotation
• Taxonomy Distribution Histogram of All Samples
• Functional Database Annotation
  Kyoto Encyclopedia of Genes and Genomes (KEGG); Version: 2018.01;
  Evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG); Version: 4.5;
  Non-Redundant Protein Sequence Database (NR);
  UniProt Knowledge base (UniProt);
  Virulence Factors Database (VFDB);
  Transporter Classification Database (TCDB);
  Pathogen Host Interactions Database (PHI);
  Carbohydrate-Active enZYmes Database (CAZy);
  The Comprehensive Antibiotic Resistance Database (CARD);
• Alpha Diversity Analysis
  Statistical Data of Alpha Diversity
  Rarefaction curve
  Chao1 curve
  Shannon curve
  Rank Abundance
• Beta Diversity Analysis
  Different algorithm distance matrix (jaccard, bray Curtis, weighted unifrac and unweighted unifrac)
  PCA Analysis
  PCoA Analysis
  ※ LEfSe
  ※ Anosim/Adonis Analysis
  UPGMA Analysis
• ※ Binning

How It Works

CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.

Table 1 Partial software and database list

Reference

1. Bharti, R., & Grimm, D. G. (2021). Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform, 22(1), 178-193. doi:10.1093/bib/bbz155