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    组装 assembly

    生物信息分析
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    • 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.

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      • 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.

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        • 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

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          • 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

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            • A
              anneng 最后由 编辑

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

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              • 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

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                • 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

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                  • 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

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                    • 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.

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                      • 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

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