TotalOmics
박테리아 유전체 해독 생명정보 분석
1. Genome survey: Genome sequencing with 50X sequencing depth would be performed to obtain the information of genome features such as GC contents, repeats, genome size and heterozygosity rate, evaluate the heterogeneous sequence result and difficulty of genome assembly for the specific species. Whether the subsequent bioinformatics analysis could be carried on is based on the survey results.
1. Raw data production
2. Data production and quality control
3. Preliminary genome assembly by SOAPdenovo
4. Assessment of assembly quality
4.1 GC content and depth correlative analysis
5. Heterogeneous sequence analysis
5.1 K-mer analysis
6. Alignment with NT database (when heterogeneous sequence exists)
2. Bacterial genome draft map
1. Bacterial genome survey
2. Standard bioinformatics analysis (Intermediate)
2.1 Genome assembly by SOAPdenovo
2.2 Assessment of assembly quality
2.3 Gene prediction
2.3.1 ab initio prediction by Glimmer 3.0 software;
2.3.2 Homology gene prediction
2.4 Gene functional annotation
2.4.1 COG, KEGG, SwissProt annotation
3.Bacterial genome fine map (Intermediate and advanced bioinformatics are optional)
1. Fungal genome survey (optional)
2. Standard bioinformatics analysis (Intermediate)
2.1 Genome assembly by SOAPdenovo
2.2 Assessment of assembly quality
2.3 Gene prediction
2.3.1 ab initio prediction by Glimmer 3.0 software
2.3.2 Homology gene prediction
2.4 Gene functional annotation
2.4.1 COG, KEGG, SwissProt annotation
3. Standard bioinformatics analysis (Advanced)
3.1 Genome assembly by SOAPdenovo
3.2 Assessment of assembly quality
3.3 Gene prediction
3.3.1 ab initio prediction by Glimmer 3.0 software;
3.3.2 Homology gene prediction
3.4 Gene functional annotation
3.4.1 KEGG, COG, SwissProt, TrEMBL, NR annotation
3.5 Repetitive sequences analysis
3.5.1 Using RepeatMasker against the known transposable elements (TE) in Repbase
3.5.2 Using TRF to find variable number tandem repeats (VNTR)
3.6 Non-coding RNAs
3.4 Fine map criteria: The genome coverage is above 95%. The coverage of gene region is above 98% (with sequence of highly relative species), the single base error rate of the assembly result less than one hundred thousandth (excluding heterozygotes site), the overall sequencing depth no less than 100 X.
3.5 Bacterial genome complete map
On the basis of bacterial fine map, clients must offer primers and we offer platform.
3.6 Personalized analysis:
1. Genome map
2. Synteny analysis (Reference needed)
3. Phylogenic analysis (Reference needed)
4. Variation analysis (Reference needed)
4.1 SNP detection
4.2 InDel detection
4.3 Horizontal gene transfer (HGT)
5. Core and pan-genome
5.1 Core and pan-genome construction
5.2 Gene prediction and annotation
6. Phylogenic analysis (Reference needed)
6.1 Phylogenic tree construction
6.2 Ka/Ks calculation
7. Other personalized analysis contents could be determined through negotiation.
3.7 Bacteria population and evolution analysis:
1. Bacterial genome fine map ( Standard bioinformatics analysis (Intermediate))
2. Variation analysis (Reference needed)
2.1 SNP detection
2.2 InDel detection
2.3 Horizontal gene transfer (HGT)
3. Core and pan-genome
3.1 Core and pan-genome construction
3.2 Gene prediction and annotation
4. Phylogenic analysis (Reference needed)
4.1 Phylogenic tree construction
4.2 Ka/Ks calculation
