SOAP

[…] checked by fastqc []. mirtools2.0 [] 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 []. annotations are added from mirbase 21 [] and rfam [] databases. the differential expression of each known mirnas from their absolute read counts are analysed by deseq2 []. differential […]

[…] of c. neopsychrotolerans sl-16 was extracted using the ctab method. the 500-bp insert library was sequenced using the illumina pe250 system. the clean reads were then assembled by soapdenovo (http://soap.genomics.org.cn, v2.04) for data processing. genes were subsequently predicted using augustus 3.2.1 and genemark-es 4.21 with default parameters, which were further integrated by the glean […]

[…] from ncbi (srr555564) and assembled into unigenes using the trinity 2.4.0 software. the snp-associated rad tag sequences were aligned against the assembled transcriptome of a. konjac using soap 2.21 with the default settings. to investigate the gene function of loci, a blastx search was applied against ncbi’s non-redundant database by blast 2.2.28 with an e-value of 1e−6. according […]

[…] rnas were used for further analysis. high‐quality clean small rna tags were mapped to tomato genome (ftp://ftp.solgenomics.net/tomato_genome/annotation/itag2.4_release/itag2.4_genomic.fasta) by soap (short oligonucleotide alignment program) to find out their expression and distribution on the genome (li et al., ). then, the matched tags were aligned to ncbi genbank […]

[…] dna was sequenced using an illumina hiseq 2000 sequencing platform (illumina, ca, usa). a total of 1,463 mb data was produced and the short reads were assembled into a genome sequence using the soap de novo method (). the total length of the draft genome was 4,077,699 bp with a mean g+c content of 35.7%. the assembly contained 26 scaffolds and 27 contigs. gene prediction was performed […]

[…] with an insertion size of 500 bp, 2 kb, and 6 kb, respectively. low-quality reads were filtered by trimmomatic []. the high-quality reads were used for de novo assembly and scaffolding using soap denovo (version 1.05, http://soap.genomics.org.cn/soapdenovo.html). gaps closure was performed using gapcloser v1.12 [, ]. the completeness of the c. pseudoreteaudii genome was evaluated using […]

[…] the most commonly used mapping algorithms used for this task include bowtie [], bowtie2 [], star [], novoalign (http://www.novocraft.com/products/novoalign/), rmap [], tophat [], gsnap [], soap [] and bwa [], some with unique advantages over others depending on whether mapping is done on a genome versus transcriptome. the choice of algorithm and the parameters for mapping will need […]

[…] of c. neopsychrotolerans sl-16 was extracted using the ctab method. the 500-bp insert library was sequenced using the illumina pe250 system. the clean reads were then assembled by soapdenovo (http://soap.genomics.org.cn, v2.04) for data processing. genes were subsequently predicted using augustus 3.2.1 and genemark-es 4.21 with default parameters, which were further integrated by the glean […]

[…] to obtain double terminal sequence of 90 bp reads. for the removal of the low-quality and polluted reads, the adapter sequence 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 […]

[…] proteins was predicted by the protcomp 9.0 program (for animals and fungi, http://www.softberry.com)., to quantify the expression of unigenes, reads were mapped to the unigene sequence using a soap aligner allowing a maximum of three mismatches in one read []. an in-house perl script was used to count the number of reads that mapped to each unigene. only the reads that uniquely mapped […]