组装 assembly
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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. -
https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assemblerhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813482/
De novo assembly of human genomes with massively parallel short read sequencing
(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. -
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083584/
Genetic anchoring of whole-genome shotgun assembliesThe process of assigning chromosomal locations to contigs of an assembly is referred to as anchoring.
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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 evaluationhttps://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022/
对synteny的解释 -
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https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04591-4
gcaPDA: a haplotype-resolved diploid assembler
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https://academic.oup.com/nar/article/44/12/e113/2457531
Redundans: an assembly pipeline for highly heterozygous genomes
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https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1911-6
Reference-guided de novo assembly approach improves genome reconstruction for related species -
https://www.frontiersin.org/articles/10.3389/fpls.2018.01660/full
Current Strategies of Polyploid Plant Genome Sequence Assembly
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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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
