“…The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. …”
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“…Transcriptomes were assembled using the Trinity de novo assembler and were annotated and the protein sequences predicted. …”
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“…METHOD: Using data from focus groups, interviews, and recorded observations, the research team systematically documented the innovation process, including themes and deviations, employing Smale’s Innovation Trinity framework to organize the larger picture. …”
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“…Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperatures. Trinity was used to create de novo assemblies for each species from 92–102 million raw Illumina Hiseq 2 × 150 bp reads. …”
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“…Transcriptome data is generated with a de novo transcriptome assembler, Trinity. Amino acid sequences are predicted from the assemblies, using TransDecoder. …”
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“…Gene Ontology term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied for the identification of pathways in which differentially expressed genes were significantly enriched. RESULTS: Trinity was used to de novo assemble the reads, and 120,664 unigenes were assembled. …”
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“…The subjects were administered the Trinity Amputation and Prosthesis Experience satisfaction scale and other usability and satisfaction measures. …”
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“…Because of the absence of a reference-grade genome for blueberry, a transcriptome was de novo assembled from this RNA-seq data and other publicly available transcriptome data from blueberry downloaded from the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) using Trinity. After removing redundancy, this resulted in a dataset of 91,861 blueberry unigenes. …”
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“…The raw reads were quality trimmed and assembled de novo using TRINITY assembler which created 156822 (control) and 148953 (diseased) contigs with N50 values 2107 (control) and 2182 (diseased). …”
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“…A combination of Illumina HiSeq 2500, Trinity, BLAST X, Bowtie 2 and BLAST 2GO was used for RNA Seq, de novo assembly, transcript annotation, gene expression estimation and gene ontology annotation respectively. …”
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“…RNA-seq data from 17 total samples representing these stages were pooled to generate a de novo assembly of the transcriptome using a Trinity pipeline. From 27.9Gb of raw sequences, we identified 21,244 transcripts. …”
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“…A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. …”
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“…Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. …”
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“…SIMPLE SUMMARY: The primary, secondary and tertiary immune sites, namely the tumour microenvironment (TME), the lymph nodes (LNs) and the peripheral blood, form the cardinal trinity of immune environments in breast cancer. With the success of immuno-therapies in some subtypes of breast cancers, an integrated understanding of these intertwined immune sites is essential to potentiate their anti-cancer responses and enhance the efficacies of therapeutic agents, and in turn, illuminate novel pathways of anti-cancer immunity and therapeutic opportunities. …”
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“…Says Dr. Mark Silverman of Trinity College in Hartford, Connecticut: "The author … introduces the mathematical methods essential to understanding and applying general relativity…but leaves to more advanced references derivations that a beginning student would likely find overly long and tedious…. …”
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“…In this paper we report experience in practical use of the program at the Trinity College Dublin. Participants could anonymously register and individually choose the length of participation in the prevention program. …”
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“…For de novo assembly, five programs were used: ABySS, Velvet, OASES, Trinity and Rnnotator. Based on a comparison of the assemblies, we chose the Rnnotator dataset for the following blast searches and gene ontology analyses. …”
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“…We obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (C. annuum) ESTs databases. …”
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“…RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. …”
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