151 lines
4.9 KiB
Markdown
151 lines
4.9 KiB
Markdown
---
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layout: section
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color: navy
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---
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<div class="w-7/10 mx-auto text-center">
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## 技术路线与分析进展
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<hr/>
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当前分析进展情况
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</div>
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---
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layout: side-title
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color: navy
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align: rm-lm
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titlewidth: is-3
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title: 技术路线图（上）
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---
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::title::
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# 技术路线图（上）
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::content::
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```mermaid
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flowchart TD
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classDef default fill:#ECF5FF,stroke:#409eff,stroke-width:2px,color:#409eff;
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classDef done fill:#F0F9EB,stroke:#67c23a,stroke-width:2px,color:#67c23a;
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classDef warn fill:#FDF6EC,stroke:#e6a23c,stroke-width:2px,color:#e6a23c
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subgraph subgraph1[Step1. 数据预处理与组装]
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direction LR
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RawData[原始数据，来自sra]:::warn --> CleanData[数据清洗与质控，Fastp]:::done
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CleanData -- 沙棘样品，有参 --> AlignData[比对到参考基因组，Hisat2]:::done
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AlignData --> Assembly[组装成转录本，Trinity]:::done
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CleanData -- 胡颓子，无参 --> Assembly[组装成转录本，使用N50和busco评估组装结果，Trinity]:::done
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end
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subgraph subgraph2[Step2. 同源基因集聚类]
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direction LR
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ass[转录本]:::warn --> CDS[预测CDS，抽取最长转录本的最长ORF作为输入CDS，TD2]:::done
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CDS --> reducedCDS[单样本CDS序列去冗余，CD-HIT]:::done
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reducedCDS --> ortho[基因家族聚类得到低拷贝同源基因集，OrthoFinder]:::done
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ortho --> homolog[将枣的同源基因整合到低拷贝同源基因集中, hmmer]:::done
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end
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subgraph subgraph3[Step3. 基因集筛选与基因树]
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direction LR
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homo[低拷贝同源基因集]:::warn --> alignment[基于蛋白序列比对，macse<br>修剪比对序列，trimAl]:::done
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alignment --> treeshrink[fasttree快速构树，基于长枝吸引（treeshrink）和比对序列长度过滤基因集]:::done
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treeshrink --> modeltest[序列进化模型检验，modeltest-ng]:::done
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modeltest --> raxml[构建ML单基因树]:::done
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modeltest --> mrbayes[构建BP单基因树]:::done
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raxml --> trees[根据mrbayes的结果收敛性筛选基因树与对应序列]:::done
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mrbayes --> trees
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end
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subgraph subgraph4[Step4. 物种系统发育关系]
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direction LR
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tree[过滤后单基因树与对应序列]:::warn -- 单基因ML树 --> coalescence[溯祖关系树, Aster]
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tree -- 单基因ML树 --> phyparts[基因树不一致性展示]
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tree -- 单基因序列 --> concatenation[串联关系树，iqtree3]
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tree -- 单基因的mrbayes分析结果 --> CFs[基因树一致性因子，BUCKy]:::done
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CFs --> network[系统发育网络，SNAQ]:::done
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coalescence --> network
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end
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subgraph note[节点说明]
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direction TB
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done[已完成分析]:::done
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warn[重要中间数据]:::warn
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default[未完成分析]
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end
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subgraph1 --> subgraph2
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subgraph2 --> subgraph3
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subgraph3 --> subgraph4
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subgraph4 ~~~ note
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```
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---
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layout: side-title
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color: navy
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align: rm-lm
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titlewidth: is-3
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title: 技术路线图（下）
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---
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::title::
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# 技术路线图（下）
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::content::
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```mermaid
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flowchart TD
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classDef default fill:#ECF5FF,stroke:#409eff,stroke-width:2px,color:#409eff;
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classDef done fill:#F0F9EB,stroke:#67c23a,stroke-width:2px,color:#67c23a;
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classDef warn fill:#FDF6EC,stroke:#e6a23c,stroke-width:2px,color:#e6a23c
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subgraph subgraph5[Step5. 叶绿体系统发育关系]
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direction LR
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cleanData[Clean Reads]:::done --> alignCp[比对到参考叶绿体基因组，hisat2]:::done
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alignCp --> callExon[提取比对上的外显子序列，samtools]
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callExon --> cpTree[串联高质量的exon片段，构建叶绿体基因组系统发育树，iqtree3]
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cpTree --> divergence[估算叶绿体基因组分歧时间，beast]
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end
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subgraph subgraph6[Step6. 沙棘模型分析]
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direction LR
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genes[筛选得到的低拷贝同源基因集]:::warn --> filterGenes[基于ml树筛选基因集用于后续模型]
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filterGenes --> mcmcTree[使用mcmctree估算分化时间]
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mcmcTree --> fitModel[使用模型拟合种间分化时间分布]
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fitModel --> integrate[整合不同模型结果得到最终分化时间估计]
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end
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subgraph subgraph7[Step7. bpp模拟模型分析]
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direction LR
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bpp[使用bpp进行溯祖模拟得到基因集]:::warn --> mcmcTreeBPP[使用mcmctree估算分化时间]
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mcmcTreeBPP --> fitModelBPP[使用模型拟合种间分化时间分布]
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fitModelBPP --> integrateBPP[整合不同模型结果得到最终分化时间估计]
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end
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subgraph subgraph8[Step8. 蛇数据分析]
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direction LR
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snakeData[蛇数据]:::warn --> mcmcTreeSnake[使用mcmctree估算分化时间]
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mcmcTreeSnake --> fitModelSnake[使用模型拟合种间分化时间分布]
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fitModelSnake --> integrateSnake[整合不同模型结果得到最终分化时间估计]
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end
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subgraph note[节点说明]
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direction TB
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done[已完成分析]:::done
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warn[重要中间数据]:::warn
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default[未完成分析]
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end
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subgraph5 --> subgraph6
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subgraph6 --> subgraph7
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subgraph7 --> subgraph8
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subgraph8 ~~~ note
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```
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