SOAPsv

[…] stop codons or splice sites. snps in coding sequences were annotated as synonymous or non-synonymous. go or pfam annotation of genes was also conducted., structural variations were detected using soapsv (version 1.02), for indel (more than 5 bp in length), replication, reversion, transposition, and other variations. the minimum read depth was set to 3., we first calculated the distances […]

[…] the reference and unmapped reads. average sequencing depth and coverage were calculated using the alignment results. the mapped reads were then used to detect snps, indels, and svs using soapsnp and soapsv software with default parameter settings.– the snps identified were filtered based on the following stringent criteria: no less than two times for coverage depth (no less than three times […]

[…] for identifying reads with abnormal insert sizes, or only one end mapped to the genome and determined a sv when more than 3 paired reads abnormally mapped. this method was implemented in the soapsv., we identified cnvs according to the mapping depth described previously. assuming a poisson’s distribution of sequencing depth, the genome regions were divided into initial windows, […]

[…] of 13× coverage was achieved (table ), and the resulting consensus sequence covered approximately 82.57% of the reference genome.table 1, 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 ). […]

[…] was removed and the purification data analyzed by sequence alignment. soap software (soapdenovo v2.04; soap3/gpu v0.01beta; soapaligner/soap2 v2.20; soapsplice v1.1; soapsnp v1.03; soapindel v1.0; soapsv v1.02) was used to analyze copy number, single nucleotide polymorphism (snp), and insertion/deletion (indel). annotations were used to screen suspected pathogenic variants. the polymorphism […]

[…] each species was determined using soapsnp v1.04 with the criteria previously reported (). small insertions and deletions were identified using soapindel v2 (), and inversions and duplications using soapsv ()., to identify splice junctions, we first aligned the filtered rna-seq reads for each falcon to the falcon reference genome using bowtie 0.12.7. splice junctions were then predicted using […]

[…] pairs of reads were required to define an indel. for indels annotation, analysis of regional information and impact of indels on cds region, such as in a frameshift mutation, was possible., the soapsv (http://soap.genomics.org.cn/soapsv.html) program was used to detect structural variations by whole genome de novo assembly system requirements. structural variations (svs) is one […]

[…] the average contig size was 49 339 ± 6088 bps., we here applied an integrative strategy to identify the svs of han chinese people, including multiple current algorithms. the assembly-based method (soapsv) [] was firstly employed in sv calling. we finally obtained a total of 26 142 svs, containing 12 772 insertions and 13 370 deletions. the average number for each individual is 3102 ± 190. […]

[…] 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 […]