Comparative Study Of SNP Detection Procedures Based On Second Generation Sequencing Technology

Object:Today,with the increasing popularity of high-throughput technology and SNP molecular marker technology,more and more research needs to obtain effective SNP genetic information from the readings produced by high-throughput sequencing technology for further research.With the further development of molecular experimental techniques,more effective,rapid and high-throughput SNP detection methods have been developed by researchers.However,there are still relatively few methods for calling various SNPs.It is still unclear what kind of sequencing strategy and what kind of SNP calling method can obtain the most effective results.This is especially true in the context of the fact that most researchers have handed this step to the sequencing company for analysis.Methods:This study compares the performance of the six SNPs calling software(Varscan,Altas-snp2,GATK,Freebayes,SOAPsnp2,and SAMtools)in two datasets,simulated datasets,and real datasets.A certain degree of interpretation has been carried out,which provides convenience for the researcher Du Yu' The results show that the results of the six SNP calling softwares are quite different:Results:in the results of SNP detection using real data,SOAPsnp can detect the most SNPs,and Freebays and Atlas-snp2 detect fewer SNPs;Whether to remove low-quality bases has an effect on this software,and removing low-quality bases can detect more SNPs;these six softwares call the SNPs with poor consistency,and dbSNPs are usually higher than non-dbSNPs.Consistency,which indicates that the quality of the identified non-dbSNPs in the low coverage sequencing data is lower.In the results of SNP detection using simulated data,the sequencing depth has a significant effect on SNP detection,while the length of sequencing reads has no significant effect on SNP detection;if only from the experimental results,the 250 bp sequencing strategy results are the best;under S× sequencing depth,except for Varscan and Altas-snp2,good results were obtained.The SNP detection rates of the other 4 softwares were all above 85%;if the sequencing depth reached 7×,basically the other software except Varscan Both can get good results,the detection rate is above 90%.And all SNP detection software SNP detection accuracy rate is above 97%,fully meet the needs of scientific research work.s current SNP calling situation.Conclusion:In general,the sequencing strategy recommended in this study is 7X sequencing depth,250bp sequencing reads length,in the SNP after the data acquisition process,this study recommends using a variety of SNP calling software combination methods in order to obtain the best The results facilitate subsequent analysis of the genome.