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

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      • 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

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        • 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.

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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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