TotalOmics
균류 유전체 해독 생명정보 분석
1. Genome survey: Genome sequencing with 30X 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. Fungal genome draft map
1. Fungal 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 Augustus, SNAP, GeneMark-ES software
2.3.2 Homology gene prediction
2.4 Gene functional annotation
2.4.1 KEGG、COG、SwissProt、TrEMBL、NR、GO annotation
3. Fungal genome fine map (Intermediate and advanced bioinformatics are optional)
1. Fungal genome survey
2. Standard bioinformatics analysis (Intermediate)
2.1 Genome assembly by SOAPdenovo
2.2 Assessment of assembly quality
2.3 Gene prediction
2.3.1ab initio prediction by Augustus, SNAP, GeneMark-ES 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 Augustus, SNAP, GeneMark-ES 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
4. Fine map criteria: The coverage of chromosome or chromatin genome is above 95%. The coverage of gene region is above 98% (with sequence of highly relative species), the scaffold sequence N50 length to 300 Kb, the single base error rate of the assembly result less than one hundred thousandth (excluding heterozygotes site), the overall sequencing depth no less than 50 X.
5. Personalized analysis:
1. Synteny analysis (Reference needed)
2. Gene family analysis (Reference needed)
3. Particular function protein annotation
3.1 Secreted protein prediction
3.2 Membrane protein annotation
4. Other personalized analysis contents could be determined through negotiation.
