SOAP

[…] checked by fastqc [54]. mirtools2.0 [55] pipeline is used for trimming (“adaptor_trim.pl” script) and downstream analysis of known mirnas. sequencing reads are aligned to the bostau7 genome using soap [56]. annotations are added from mirbase 21 [57] and rfam [58] databases. the differential expression of each known mirnas from their absolute read counts are analysed by deseq2 [34]. […]

[…] from ncbi (srr555564)33 and assembled into unigenes using the trinity 2.4.0 software48. the snp-associated rad tag sequences were aligned against the assembled transcriptome of a. konjac using soap 2.2149 with the default settings. to investigate the gene function of loci, a blastx search was applied against ncbi’s non-redundant database by blast 2.2.2850 with an e-value of 1e−6. according […]

[…] reactions were performed according to the manufacturer’s instructions and a 300 pair-end library was generated. the resulting sequences were de novo assembled using soapdenovo v2.01 (http://soap.genomics.org.cn/) (6). for the prokaryotic organism, we used an ab initio prediction method to get gene models for strain av208. gene models were identified using glimmer 3 (7). then, all gene […]

[…] with poly (a) or simple repeats, and (6) reads shorter than 18 nt. the clean reads were screened against and mapped to the latest ovine genome assembly (oar_v3.1, released sept. 20, 2012) using the soap program (soap aligner v2.21, http://soap.genomics.org.cn/)37. after mapping, we used the clc genomics workbench 5.5 tool to blast the clean reads against the rfam database […]

[…] or simple repeats, and (6) reads shorter than 18 nt. the clean reads were screened against and mapped to the latest ovine genome assembly (oar_v3.1, released sept. 20, 2012) using the soap program (soap aligner v2.21, http://soap.genomics.org.cn/)37. after mapping, we used the clc genomics workbench 5.5 tool to blast the clean reads against the rfam database […]