多倍体的SNP
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791807/
SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species -
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555216/
SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Cropshttps://edepot.wur.nl/441939
SNP detection in
allopolyploid crops
using NGS data
这篇文章对sweep做了评估 -
https://www.biorxiv.org/content/10.1101/2022.04.21.488948v1.full
CAPG: Comprehensive Allopolyploid Genotyper
异源四倍体SNP的2种类型
Distinguishing homoeologous and allelic SNPs.
Allotetraploid genomes for two individuals, subgenome A (left), subgenome B (right). Pink loci are homoeologous SNPs, different between and constant within subgenomes. Other colored loci are allelic SNPs, green in subgenome A, red in subgenome B. The dark green and brown loci are homozygous. The light green and red loci are heterozygous in one of the individuals. -
https://www.cerealsdb.uk.net/cerealgenomics/WheatBP/Documents/DOC_Homoeologous_vs_Varietal_SNPs.php#:~:text=a)%20A%20homoeologous%20SNP%20exist,characteristic%20of%20a%20single%20individual.
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https://sci-hub.st/10.1007/s00438-008-0365-y
Identification of homologous, homoeologous and paralogous sequence variants in an outbreeding allopolyploid species based on comparison with progenitor taxa -
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https://max.book118.com/html/2014/0318/6706569.shtm
多倍体植物中单核苷酸多态性（SNPs）的开发 -
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920642/
Homoeologs: What Are They and How Do We Infer Them?
Homoeologs are pairs of genes that originated by speciation and were brought back together in the same genome by allopolyploidization.
Homoeologs are not necessarily one-to-one or positionally conserved.
部分同源指的是基因经过不同的演化后，又因为异源杂交，被放到了同一个基因组中。
allopolyploids result from genome doubling following a hybridization between two different species (interspecific), whereas autopolyploids result from genome doubling within one species (intraspecific).
https://lab.dessimoz.org/blog/2016/03/24/what-are-homoeologs
Last but not least, we learned that even though homoeolog has alternatively been spelled “homeolog” (no extra o), homoeolog is the clear winner in terms of popularity.
homoeolog有时候也被写作homeolog -
genes-11-01220-v2.pdf
这个文献研究了花生 花生也是一个异源四倍体 相似的文献可以重点看看
这个流程结合了GATK+Sweep -
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062318/
Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica -
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SNP Discovery in Complex Allotetraploid Genomes
(Gossypium spp., Malvaceae) Using Genotyping by
Sequencing
apps.1400077.pdf -
A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-100 -
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https://gist.github.com/sbamin/27acf13f2a28161efbf89a273559bca4
https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignmentsambamba view -t 12 -h -f bam -F "mapping_quality >= 1 and not (unmapped or secondary_alignment) and not ([XA] != null or [SA] != null)" test.bwa-mem.bam -o test-uniq.bam获取唯一比对的序列
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Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut
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https://www.frontiersin.org/articles/10.3389/fgene.2020.00222/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Genetics&id=521391
Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut该文献对异源多倍体的snp分析对比了5种流程 可以重点看看
