Molecular markers 分子标记

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Molecular markers are DNA sequences that can be identified and inherited and are present in
certain locations in the genome and characterize certain characteristics.
Mining_and_characterization_of_genomic-based_micro.pdf

分子标记要可识别、可遗传、位置固定且能表达一定的特征。
DNA
markers without PCR (Polymerase Chain Reaction) such as RFLP, second, DNA markers based on
PCR which include RAPD, AFLP, SSR, CAPS, SCAR, SSCP and DNA Barcoding
分子标记分为：
1.非PCR方式，如RFLP
2.PCR方式，如RAPD, AFLP, SSR, CAPS, SCAR, SSCP and DNA Barcoding

Microsatellite markers are codominant,the quantity of DNA needed is not much, the method used is quite simple and widely available in the market.
微卫星是一种共显性的标记。
什么是共显性？

单核苷酸重复用的比较少通常用6核苷酸二、三重复最普遍

Microsatellites can be categorized based on their motifs with the composition: i) perfect, if the
whole consists of repetition of single motive; ii) imperfect, if base pairs are not included in the motive
to occur between repetitions; iii) interrupted if the order of some base pairs is included in the motif; or
iv) composite if formed by many, close together, repetitive motifs

The Assembly-stat program is used to calculate contig statistics. The
contigs having minimum filtering of 200 bp and filtering from the redundancy contig using the CAP3
and CD-hit programs. MISA program is used to identify content containing microsatellite with
minimum repetitions: 10 for 1 basis, 6 for 2 bases, and 5 for 3, 4, 5, and 6 bases; and interruptions (the
maximum difference between microsatellites) are 100 bases.

https://academic.oup.com/bioinformatics/article/33/16/2583/3111841

https://github.com/cfljam/SSR_marker_design

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https://www.sciencedirect.com/science/article/pii/S0888754318303914
PLANET-SNP pipeline: PLants based ANnotation and Establishment of True SNP pipeline
该文献比较了5种ML算法， Naive Bayes, Random Forest, J48, Bayes Net and SVM. 来降低SNP的假阳性。

1.Freebayes
使用uniquely mapped reads Freebayes可以对多等位的SNP进行分析。
针对异源四倍体 allotetraploid 做了额外的分析。

2.模型过滤

3.VCF注释

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An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data

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GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data