Page 5 - Omics
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Analysis Process                   3       Illumina DNA-Seq                                                                                         Gene families
                                1                                            FastQC

           Tissues (Mussel）                       Quality Control                                                                                    Family expansion and
                                                                                                                                                           contraction


          Illumina DNA-Seq                        HiCUP Truncater                                                                                     Phylogenetic analysis       5



            Quality Control                                                                                                                        Time of species divergence
                                                   HiCUP Mapper

                                                                          HiCUP
     Genome size                                    HiCUP Filter                                                                                    Positive selection analysis
     Genome pollution Genome
     heterozygosity
                                                HiCUP Deduplicator                                                                                    4

                                                                                                                                            Genome Annotation
                                                      Di-Tags

                   2                  ALLHiC
                                                  Contig/Scaffold
          PacBio SMRT-Seq


                                                   Chromosomes
          Polymerase Reads



              HiFi Reads
                                             1.  BUSCO评估: 使用tblastn、augustus 、hmmer比对基
                                      Hifiasm
                                                 因组到单拷贝直系同源基因库
             Contig (N50)
                                             2.  CEGMA 评估: 使用tblastn、genewise、geneid比对基

                                                 因组到6个真核模式生物中的248个保守基因构成的
            Scaffold (N50)
                                                 Core Gene库
                                             3.  序列一致性: 使用BWA 比对Illumina Reads到组装的
         Assembly evaluation                     基因组，计算覆盖率和比对率
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