暗能星系
    • 登录
    • 搜索

    组装 assembly

    生物信息分析
    1
    14
    32
    正在加载更多帖子
    • 从旧到新
    • 从新到旧
    • 最多赞同
    回复
    • 在新帖中回复
    登录后回复
    此主题已被删除。只有拥有主题管理权限的用户可以查看。
    • A
      anneng 最后由 anneng 编辑

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503144/
      Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
      most assemblers output a “mosaic” genome sequence that arbitrarily alternates between parental alleles
      大多数组装软件随意拼接了等位基因。
      为什么人是2倍体，但是参考基因组只有一组？
      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305238/
      Extending reference assembly models
      Employing a clone-based approach, the sequence of each clone represented a single haplotype from a given donor. At clone boundaries, however, haplotypes could switch abruptly, creating a mosaic structure. This design introduced errors within regions of complex structural variation, when sequences unique to one haplotype prevented construction of clone overlaps.
      Many alignment and analysis tools penalize reads that align to more than one location under the assumption that the location of these reads cannot be resolved owing to paralogous sequences in the genome. These tools do not distinguish allelic duplication, added by the alternative loci, from paralogous duplication found in the genome, thus confounding repeat and mappability calculations, paired-end placements and downstream interpretation of alignments in regions with alternative loci.
      软件在比对时 无法区分reads到底比对到了哪个同源序列上

      https://en.wikipedia.org/wiki/Reference_genome#:~:text=As they are assembled from,DNA sequences from each donor.
      As they are assembled from the sequencing of DNA from a number of individual donors, reference genomes do not accurately represent the set of genes of any single individual organism. Instead a reference provides a haploid mosaic of different DNA sequences from each donor.

      https://www.bio-itworld.com/news/2014/06/30/the-hunt-for-a-new-human-reference-genome

      1 条回复 最后回复 回复 引用 0
      • A
        anneng 最后由 编辑

        https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227110/
        Assemblathon 1: A competitive assessment of de novo short read assembly methods

        1 条回复 最后回复 回复 引用 0
        • A
          anneng 最后由 编辑

          https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1774-4
          Is it time to change the reference genome?
          a consensus genome represents the most common alleles and variants within a population
          5097c16f-d4d2-420c-8537-4150e1b78970-image.png

          1 条回复 最后回复 回复 引用 0
          • A
            anneng 最后由 编辑

            https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022571/
            A graph-based approach to diploid genome assembly
            However, across the short, long and hybrid categories, most assemblers require collapsing the two genome sequences of a diploid sample into a single haploid ‘consensus’ sequence (or primary contig). The consensus sequence is obtained by merging the distinct alleles at regions of heterozygosity into a single allele, and therefore losing a lot of information. The resulting haploid de novo assembly does not represent the true characteristics of the diploid input genome.

            1 条回复 最后回复 回复 引用 0
            • A
              anneng 最后由 编辑

              https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18
              SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

              https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813482/
              De novo assembly of human genomes with massively parallel short read sequencing
              79ebf8d4-6491-4e5b-a5b0-a6c41df531db-image.png

              (iv) merging the bubbles that were caused by repeats or heterozygotes of diploid chromosomes.
              soapdenovo（其他软件类似）有个步骤就是合并杂合 所以组装出来的就是单倍体

              Merging bubbles
              We used Dijkstra's algorithm to detect bubbles, which is similar to the “Tour-bus” method in Velvet. We merged the detected bubbles into a single path if the sequences of the parallel paths were very similar; that is, only had a single base pair difference or had fewer than four base pairs difference with >90% identity.

              1 条回复 最后回复 回复 引用 0
              • A
                anneng 最后由 编辑

                https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083584/
                Genetic anchoring of whole-genome shotgun assemblies

                The process of assigning chromosomal locations to contigs of an assembly is referred to as anchoring.

                1 条回复 最后回复 回复 引用 0
                • A
                  anneng 最后由 编辑

                  Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species.
                  Inferring synteny between genome assemblies: a systematic evaluation

                  https://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022/
                  e6066e1e-7016-4073-8ec4-0ac1b443955b-image.png
                  4360e495-f9ff-45c5-94bf-5020f166e708-image.png
                  对synteny的解释

                  1 条回复 最后回复 回复 引用 0
                  • A
                    anneng 最后由 编辑

                    https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-background/#de-novo-assembly-with-velvet-and-the-velvet-optimiser
                    3b8dccca-b66e-4633-b7e3-4f9c620e91ae-image.png

                    1 条回复 最后回复 回复 引用 0
                    • A
                      anneng 最后由 编辑

                      https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/

                      1 条回复 最后回复 回复 引用 0
                      • A
                        anneng 最后由 anneng 编辑

                        https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04591-4
                        gcaPDA: a haplotype-resolved diploid assembler
                        92942982-0499-44cf-a023-3d7599a9c336-image.png

                        1 条回复 最后回复 回复 引用 0
                        • A
                          anneng 最后由 编辑

                          https://academic.oup.com/nar/article/44/12/e113/2457531
                          Redundans: an assembly pipeline for highly heterozygous genomes
                          3aa8c9e4-7c9a-40a2-a5e4-1eedc6fe5858-image.png

                          1 条回复 最后回复 回复 引用 0
                          • A
                            anneng 最后由 编辑

                            35053ca0-3d16-4ce8-9a3e-24c0769de794-image.png
                            https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1911-6
                            Reference-guided de novo assembly approach improves genome reconstruction for related species

                            1 条回复 最后回复 回复 引用 0
                            • A
                              anneng 最后由 anneng 编辑

                              https://www.frontiersin.org/articles/10.3389/fpls.2018.01660/full
                              Current Strategies of Polyploid Plant Genome Sequence Assembly
                              b3073fe2-369b-4a0a-9424-02f4f2da6307-image.png
                              9669a283-455a-42ff-9485-07a0e92593f7-image.png

                              A reference genome is a digital, linear nucleic acid sequence containing only a single set of chromosomes plus any unanchored heterozygous contigs and/or scaffolds. A reference genome is used to observe variations across different individuals within a species, to study evolution and to aid genome assembly.

                              1 条回复 最后回复 回复 引用 0
                              • A
                                anneng 最后由 编辑

                                https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/
                                从这个文章看 quast可以使用参考基因组进行质控 busco可以使用同系物进行质控

                                1 条回复 最后回复 回复 引用 0
                                • First post
                                  Last post
                                Powered by 暗能星系