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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