Sentence examples for using the trinity assembler from inspiring English sources
Illumina reads of R. magnacalcarata, R. socialis, R. sordida and R. tardigrada transcriptomes were assembled using the Trinity assembler into libraries containing 60,542, 71,102, 84,989 and 121,350 transcript contigs, with a mean length of 732, 722, 830 and 714 bp, respectively.
When all sequencing reads were combined and assembled de novo using the Trinity assembler, 91,701 contigs were obtained, which represented 52,599 gene models.
De novo assembly of RNA-Seq data was carried out using the Trinity assembler, as previously described [ 62].
Using the Trinity assembler software [ 28], short-read sequences from A. konjac and A. bulbifer were assembled into 187,459 contigs and 199,259 contigs, respectively (Table 1).
> The assembly of the transcriptome from the leaf, root, seedling, flower, secondary xylem of teak branch and stem was performed using the Trinity assembler [ 35].
The de novo assembly (without a reference) was performed using reads that did not map against the public data set (previously described) using the Trinity assembler [ 68]; contigs of at least 200 bp were allowed, and the parameter "--run_butterfly" was used.
We also used the Trinity assembler to process Illumina sequences.
We chose to use the Trinity assembler, able to efficiently recover full length transcripts across a broad range of expression levels but somewhat redundant because of the inclusion of alternatively spliced variants [ 39].
Initially, a total of 486,622 transcripts were assembled using the Trinity de novo assembler.> In most previous transcriptome studies in P. ginseng, other types of housekeeping and regulatory RNAs were not eliminated from the assembled transcripts.
This approach is used by the Trinity assembler to find all spliced isoforms and transcripts of recently duplicated genes from transcriptomes (Grabherr et al., 2011).
The HQ reads of each sample library were assembled using the Trinity software [ 20] and the TGI Clustering Tool TGICLL) [ 21], followed by the Phrap assembler [ 22] to remove redundant Trinity-generated contigs.
