SOAPsv

[…] an Chinese genomesProject home page: https://github.com/HaoxiangLin/WGS_of_Han_Chinese_genomesOperating system(s): LinuxProgramming language: Shell, Perl, Java, and C++Other requirements: BWA, 0.6.1; SOAPsv, 1.02; SOAPdenovo2; PINDEL, 0.2.4t; cnvnator, 0.2.7; Breakdancer-max, 1.2; Genome STRIP, v. 1.0; SAMtools, 0.1.18; Picard, 1.61; GATK, 2.7; BEAGLE, v. 3License: GNU General Public License v.3.0 […]

[…] g sequence data were uniquely aligned to the reference longan genome. SNPs, indels, and sequence variations were identified using SOAPsnp (http://soap.genomics.org.cn/soapsnp.html), SOAPindel [], and SOAPsv [].We used all and high-quality SNPs to infer the phylogeography and population structure for D. longan. A phylogenetic tree was subsequently generated using the neighbor-joining method impleme […]

[…] e conducted whole-genome alignments between each assembly and GRCh38 using LASTZ. Then, the whole-genome alignment results were corrected and re-aligned based on a dynamic-programming algorithm using SOAPsv package. SVs that could be derived from possible misassembles were filtered out by comparing the S/P ratio for each SV region in the assembly and GRCh38; authentic SVs would be covered by suffi […]

[…] nce genome using the BLAT program. The mapped scaffolds were then aligned to the human reference genome again by using the LASTZ program () for precise mapping. SV candidates were called by using the SOAPsv program (http://soap.genomics.org.cn). Large insertions/deletions (>100 bp), the largest proportion of the SV candidates, were finally filtered by S/P ratio (number of single-end mapped reads/n […]

[…] tive depth of 13× coverage was achieved (Table ), and the resulting consensus sequence covered approximately 82.57% of the reference genome.Genome-wide variations were then examined via SOAPsnp11 and SOAPsv using a conservative quality filter pipeline (Li et al. []), and 307 627 SNPs, 57 372 InDels, and 3 096 SVs were yielded from the 7302R genome (Table , Additional files and ). We have previous […]

[…] ion covered approximately 84.8% of the reference genome (84%–85.99%), indicating a close relationship between the samples and cultivar 9311.SNPs, InDels, and SVs were then examined with SOAPsnp11 and SOAPsv using a conservative quality filter pipeline , yielding 267,383 SNPs from the genome of IR24, 288,764 SNPs from that of MH63, and 259,862 SNPs from that of SH527 (, http://rice.sicau.edu.cn/re- […]