H > ¼ºñ½º > Next-Generation Sequencing (NGS) > Metagenomic survey
Metagenomic survey
Metagenomic Survey ?
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- Metagenomics
- Microorganism classification
- Microorganism population study
- Species identification
- Gene function annotation
- Association study / pathway analysis
Metagenomic survey vs. 16s rDNA tagging
Sequencing target |
Sequencing methods |
Data | |
---|---|---|---|
16s rRNA tagging |
16s rRNA hypervariable regions |
Roche 454 | 1.Taxonomic classification
2.OTU analysis
|
Whole genome metagenomic survey |
Whole bacterial genomes |
Illumina HiSeq | 1.Species identification
2.Gene prediction
3.ORF/functional annotation |
ChIP-Seq - ½ÇÇè ÁøÇà °úÁ¤
Sample requirements
concentration | Concentration (ng/§¡) | Quality | |
---|---|---|---|
Genomic DNA | > 5§¶ (in general) | > 50 | OD(260/280)>1.8 is highly recommended |
Sequencing Strategy
91 ~ 101 PE sequencing |
Bioinformatic analysis - contents
contents | |
---|---|
1Â÷ ºÐ¼® |
1. Remove the low-quality reads 2. Remove the adapters 3. Statistics for host contamination rate £¨If host genome sequence is known£© 4. Assembly 4.1 Statistics of assembly results 4.2 Statistics of Contigs' length distribution 5. Complexity analysis of sample 5.1 Statistical table of reads usage for assembly 5.2 Kmer level estimate and GC-depth analysis 5.3 Statistical for reads alignment to known bacterial genome database, RDP database, fungal genome database, human gut gene catalogue etc. |
2Â÷ ºÐ¼® | 1. Species classification analysis and functional annotation 2. Primary comparative analysis: 3. Advanced comparative analysis |