# Knowledge Base

## Knowledge Base

- [Overview](https://kb.ezbiocloud.net/home/overview.md): Welcome to our knowledge base. Here you can explore a wealth of educational content relating to biology and bioinformatics.
- [Highlights](https://kb.ezbiocloud.net/home/highlights.md): Here we share some of the recent highlights from EzBioCloud.
- [Science Blogs](https://kb.ezbiocloud.net/home/science-blogs.md): Welcome to our educational blog. We simplify the complex world of microorganisms in and around us, highlighting how computational methods help uncover their secrets and discover patterns.
- [Basics](https://kb.ezbiocloud.net/home/science-blogs/basics.md)
- [Species](https://kb.ezbiocloud.net/home/science-blogs/basics/species.md)
- [Species Taxonomy](https://kb.ezbiocloud.net/home/science-blogs/basics/species-taxonomy.md)
- [Chimeras](https://kb.ezbiocloud.net/home/science-blogs/basics/chimeras.md)
- [Average Nucleotide Identity](https://kb.ezbiocloud.net/home/science-blogs/basics/average-nucleotide-identity.md)
- [OrthoANI](https://kb.ezbiocloud.net/home/science-blogs/basics/orthoani.md)
- [Genetic Resolution](https://kb.ezbiocloud.net/home/science-blogs/basics/genetic-resolution.md): Why does genetic resolution matter in taxonomy?
- [Identify](https://kb.ezbiocloud.net/home/science-blogs/identify.md): focus : isolates  |  process : identification  |  level : genome/16S
- [16S rRNA](https://kb.ezbiocloud.net/home/science-blogs/identify/16s-rrna.md): What is the 16S rRNA gene and its significance?
- [Identification with 16S rRNA](https://kb.ezbiocloud.net/home/science-blogs/identify/identification-with-16s-rrna.md): How can the 16S rRNA gene be used to identify bacterial species?
- [16S rRNA Resolution](https://kb.ezbiocloud.net/home/science-blogs/identify/16s-rrna-resolution.md)
- [16S rRNA Database](https://kb.ezbiocloud.net/home/science-blogs/identify/16s-rrna-database.md): Which database do we use for 16S rRNA sequences?
- [Genome Identification](https://kb.ezbiocloud.net/home/science-blogs/identify/genome-identification.md)
- [Genome Identification Process](https://kb.ezbiocloud.net/home/science-blogs/identify/genome-identification-process.md)
- [Multi-Locus Sequence Typing](https://kb.ezbiocloud.net/home/science-blogs/identify/multi-locus-sequence-typing.md)
- [16S vs Genome Identification](https://kb.ezbiocloud.net/home/science-blogs/identify/16s-vs-genome-identification.md): 16S rRNA versus Genome Identification
- [Subspecies](https://kb.ezbiocloud.net/home/science-blogs/identify/subspecies.md)
- [Phylogenomic Trees](https://kb.ezbiocloud.net/home/science-blogs/identify/phylogenomic-trees.md)
- [Genome Database](https://kb.ezbiocloud.net/home/science-blogs/identify/genome-database.md)
- [Quality Control](https://kb.ezbiocloud.net/home/science-blogs/identify/quality-control.md): What are the quality control standards for 16S rRNA and genome sequences?
- [Profile](https://kb.ezbiocloud.net/home/science-blogs/profile.md): focus : microbiome | process : profiling | level : metagenome
- [Tetra-Nucleotide Frequencies](https://kb.ezbiocloud.net/home/science-blogs/profile/tetra-nucleotide-frequencies.md): How are Tetra-Nucleotide Frequencies used in microbiome profiling?
- [16S Copy Number](https://kb.ezbiocloud.net/home/science-blogs/profile/16s-copy-number.md)
- [Up-to-date Bacterial Core Genes](https://kb.ezbiocloud.net/home/science-blogs/profile/up-to-date-bacterial-core-genes.md)
- [UBCG Technical Guide](https://kb.ezbiocloud.net/home/science-blogs/profile/ubcg-technical-guide.md): This page leads you through all the details of the Up-to-date Bacterial Cores: what they are and how to use them.
- [UBCG Set](https://kb.ezbiocloud.net/home/science-blogs/profile/ubcg-set.md): Here you can see which genes compose the Up-to-date Bacteria Core Gene set.
- [Depth of Sequencing](https://kb.ezbiocloud.net/home/science-blogs/profile/depth-of-sequencing.md)
- [Metagenome-Assembled Genomes Suitability](https://kb.ezbiocloud.net/home/science-blogs/profile/metagenome-assembled-genomes-suitability.md)
- [16S Versus Metagenomic Sequencing](https://kb.ezbiocloud.net/home/science-blogs/profile/16s-versus-metagenomic-sequencing.md)
- [Microbiomes](https://kb.ezbiocloud.net/home/science-blogs/profile/microbiomes.md)
- [Detect](https://kb.ezbiocloud.net/home/science-blogs/detect.md): focus : pathogens  |  process : detection  |  level : metagenome
- [Clinical Metagenomics](https://kb.ezbiocloud.net/home/science-blogs/detect/clinical-metagenomics.md): From Genomic Data to Clinical Classifications
- [Inferring with Amplicons](https://kb.ezbiocloud.net/home/science-blogs/detect/inferring-with-amplicons.md)
- [Pathogenicity Markers](https://kb.ezbiocloud.net/home/science-blogs/detect/pathogenicity-markers.md)
- [Antimicrobial Resistance](https://kb.ezbiocloud.net/home/science-blogs/detect/antimicrobial-resistance.md)
- [Clinical Report Process](https://kb.ezbiocloud.net/home/science-blogs/detect/clinical-report-process.md)
- [Defining a Pathogen](https://kb.ezbiocloud.net/home/science-blogs/detect/defining-a-pathogen.md)
- [Human Pathogens](https://kb.ezbiocloud.net/home/science-blogs/detect/human-pathogens.md)
- [in silico Serotyping](https://kb.ezbiocloud.net/home/science-blogs/detect/in-silico-serotyping.md)
- [Analyze](https://kb.ezbiocloud.net/home/science-blogs/analyze.md): focus : microbiome  |  process : analysis  |  level : dataset
- [Alpha Diversity](https://kb.ezbiocloud.net/home/science-blogs/analyze/alpha-diversity.md)
- [Beta Diversity](https://kb.ezbiocloud.net/home/science-blogs/analyze/beta-diversity.md): Discover the taxonomic relationships between multiple sample profiles
- [Co-occurrence](https://kb.ezbiocloud.net/home/science-blogs/analyze/co-occurrence.md)
- [Enterotyping](https://kb.ezbiocloud.net/home/science-blogs/analyze/enterotyping.md)
- [Taxonomic Composition](https://kb.ezbiocloud.net/home/science-blogs/analyze/taxonomic-composition.md)
- [reAnalyze](https://kb.ezbiocloud.net/home/science-blogs/reanalyze.md)
- [reAnalyze #1 - Skin Disease](https://kb.ezbiocloud.net/home/science-blogs/reanalyze/reanalyze-1-skin-disease.md)
- [reAnalyze #2 - Skin Ageing](https://kb.ezbiocloud.net/home/science-blogs/reanalyze/reanalyze-2-skin-ageing.md)
- [PreAnalyze #3 - Scalp Dandruff](https://kb.ezbiocloud.net/home/science-blogs/reanalyze/preanalyze-3-scalp-dandruff.md)
- [Protocols](https://kb.ezbiocloud.net/home/protocols.md): Welcome to EzBioCloud's protocol page. The following guides will lead you through how to use each tool.
- [16S Identification](https://kb.ezbiocloud.net/home/protocols/16s-identification.md): 16S rRNA species-level identification on EzBioCloud
- [Get Started](https://kb.ezbiocloud.net/home/protocols/16s-identification/get-started.md)
- [Prepare Samples](https://kb.ezbiocloud.net/home/protocols/16s-identification/prepare-samples.md)
- [Private Samples](https://kb.ezbiocloud.net/home/protocols/16s-identification/prepare-samples/private-samples.md)
- [Public Samples](https://kb.ezbiocloud.net/home/protocols/16s-identification/prepare-samples/public-samples.md)
- [Navigate Menu](https://kb.ezbiocloud.net/home/protocols/16s-identification/navigate-menu.md)
- [Upload Data](https://kb.ezbiocloud.net/home/protocols/16s-identification/upload-data.md)
- [Single Upload](https://kb.ezbiocloud.net/home/protocols/16s-identification/upload-data/single-upload.md)
- [Batch Upload](https://kb.ezbiocloud.net/home/protocols/16s-identification/upload-data/batch-upload.md)
- [Download Report](https://kb.ezbiocloud.net/home/protocols/16s-identification/download-report.md)
- [Review Report](https://kb.ezbiocloud.net/home/protocols/16s-identification/review-report.md)
- [Genome Identification](https://kb.ezbiocloud.net/home/protocols/genome-identification.md)
- [Get Started](https://kb.ezbiocloud.net/home/protocols/genome-identification/get-started.md)
- [Prepare Samples](https://kb.ezbiocloud.net/home/protocols/genome-identification/prepare-samples.md)
- [Private Samples](https://kb.ezbiocloud.net/home/protocols/genome-identification/prepare-samples/private-samples.md)
- [Public Samples](https://kb.ezbiocloud.net/home/protocols/genome-identification/prepare-samples/public-samples.md)
- [SRA Samples](https://kb.ezbiocloud.net/home/protocols/genome-identification/prepare-samples/sra-samples.md)
- [Navigate Menu](https://kb.ezbiocloud.net/home/protocols/genome-identification/navigate-menu.md)
- [Upload Data](https://kb.ezbiocloud.net/home/protocols/genome-identification/upload-data.md): To find the precise identity of your isolate, follow along with this guide using your raw isolate data or practice with the example files, provided.
- [Whole Genome](https://kb.ezbiocloud.net/home/protocols/genome-identification/upload-data/whole-genome.md): Assembled genome sequences (FASTA files)
- [Illumina](https://kb.ezbiocloud.net/home/protocols/genome-identification/upload-data/illumina.md): Unassembled isolate genome sequences (short reads, single- or paired-end FASTQ files)
- [Nanopore](https://kb.ezbiocloud.net/home/protocols/genome-identification/upload-data/nanopore.md): Unassembled isolate genome sequences (long reads, single-end FASTQ files)
- [Download Report](https://kb.ezbiocloud.net/home/protocols/genome-identification/download-report.md)
- [Copy of Review Report](https://kb.ezbiocloud.net/home/protocols/genome-identification/copy-of-review-report.md)
- [Shotgun Microbiome](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome.md)
- [Get Started](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/get-started.md)
- [Download Samples](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/download-samples.md)
- [NCBI Route](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/download-samples/ncbi-route.md)
- [Linux Route](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/download-samples/linux-route.md)
- [Navigate Menus](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/navigate-menus.md)
- [Create Studies](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/create-studies.md)
- [Profile Samples](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/profile-samples.md)
- [Describe Profiles](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/describe-profiles.md)
- [Retrieve Metadata](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/describe-profiles/retrieve-metadata.md)
- [Organize Metadata](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/describe-profiles/organize-metadata.md)
- [Upload Metadata](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/describe-profiles/upload-metadata.md)
- [Create Datasets](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/create-datasets.md)
- [Analyze Datasets](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets.md)
- [Quality Check](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/quality-check.md)
- [Pie Chart Composition](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/pie-chart-composition.md)
- [Summary Statistics](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/summary-statistics.md)
- [Group Composition](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/group-composition.md)
- [Alpha Diversity](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/alpha-diversity.md)
- [Beta Diversity](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/beta-diversity.md)
- [Differential Abundance](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/differential-abundance.md)
- [Enterotype](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/enterotype.md)
- [Co-occurrence](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/co-occurrence.md)
- [Co-occurrence Spearman](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/co-occurrence-spearman.md)
- [Statistical Matching](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/statistical-matching.md)
- [LEfSe](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/lefse.md)
- [Metadata EDA](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/metadata-eda.md)
- [Profile EDA](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/profile-eda.md)
- [Clinical Metagenomics](https://kb.ezbiocloud.net/home/protocols/clinical-metagenomics.md)
- [Dr. Chun's Lectures](https://kb.ezbiocloud.net/home/dr.-chuns-lectures.md): Welcome to Dr. Chun's Lectures page.
- [Tools](https://kb.ezbiocloud.net/home/tools.md): Welcome to EzBioCloud's Tool Suite. Several bioinformatics tools are provided as a web service or standalone software to support your specific needs.
- [Taxonomy](https://kb.ezbiocloud.net/home/taxon_name.md): Welcome to EzBioCloud's proprietary database covers the taxonomy and nomenclature of over 150,000 taxa.
- [FAQs](https://kb.ezbiocloud.net/home/faqs.md): Welcome to our Frequently Asked Questions page. For any further inquiries, feel free to send us a message!
- [Identification](https://kb.ezbiocloud.net/home/faqs/identification.md)
- [Clinical Metagenomics](https://kb.ezbiocloud.net/home/faqs/clinical-metagenomics.md)
- [Privacy Policy](https://kb.ezbiocloud.net/home/faqs/privacy-policy.md)
- [Terms of Service](https://kb.ezbiocloud.net/home/faqs/terms-of-service.md)