“…After evaluating several trimming and transcript reconstruction strategies, de novo assembly using Trinity uncovered 42,459 unique contigs containing at least a partial protein-coding sequence based on alignment to a reference set of known Actinopterygii sequences. …”
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“…Sequences were assembled de novo using trinity resulting in 64,438 transcripts which were classified into 32,204 unigenes comprising of 9853 clusters and 22,351 singletons. …”
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“…Illumina sequencing and Trinity assembly generated 68,010 unigenes (mean length of 911 bp), of which 32.8 % were annotated to the RefSeq plant database. …”
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“…This study compared four transcriptome assembly methods, including a widely used de novo assembler (Trinity), two transcriptome re-assembly strategies utilizing proteomic and genomic resources from closely related species (reference-based re-assembly and TransPS) and a genome-guided assembler (Cufflinks). …”
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“…A combined assembly of 92,772 transcripts was produced de novo using the Trinity programme. About 18,000 transcripts were annotated with at least one GO (gene ontology) term. …”
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“…RESULTS: Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively. Trinity assembly of the reads resulted in 98,317 transcripts for Ib and 275,044 for It, after post-assembly removal of trans-chimeras. …”
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“…Using simulated data, we show that this strategy is significantly more sensitive and precise than the previous version of KisSplice (Sacomoto et al. in WABI, pp 99–111, 1), Trinity (Grabherr et al. in Nat Biotechnol 29(7):644–652, 2), and Oases (Schulz et al. in Bioinformatics 28(8):1086–1092, 3), for the specific task of calling AS events. …”
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“…The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. …”
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“…The transcriptome of T. mentagrophytes was sequenced by using Illumina HiSeq™ 2000 technology and the de novo assembly of the transcriptome was performed by using the Trinity method, and functional annotation was analyzed. …”
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“…De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. …”
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“…The performance of the fluorescent spot test (Trinity, Ireland; FST) and a G6PD RDT (Carestart, USA) against spectrophotometry were assessed. …”
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“…RESULTS: A total of 91.7, 100.3 and 100.1million clean reads were acquired for the leaf, branch and capsule, respectively; and 85,342 unigenes with a mean length of 893.60 bp and N50 length of 1307 nt were assembled using Trinity program. BLASTx analysis allowed to annotate 40,218 unigenes using public protein databases, including NR, KOG/COG/eggNOG, Swiss-Prot, KEGG and GO. …”
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“…The transcriptome de novo assembly and Unigene expression determination were conducted using Trinity, Tgicl, Bowtie2, and RSEM software. The differentially expressed transcripts were functionally annotated mainly through COG, GO, and KEGG databases. …”
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“…RESULTS: Following the PacBio standard analysis pipeline, 66,046 polished consensus sequences were obtained, while Illumina data were assembled into 140,601 unigenes with Trinity software. Then, these output sequences from the two analytical routes were merged. …”
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“…We monitor spread to the neighboring suburb of Trinity Park to assess confinement. Results suggest that translocations could be introduced on a suburban scale, and remediated through releases of non-disease-transmitting male mosquitoes with release sizes on the scale of what has been previously implemented. …”
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“…To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). …”
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“…CCA ordination showed distinguishable clustering patterns between southern California counties (Santa Clara, Santa Cruz, Alameda, and San Diego) and northern coast and Klamath mountains range (Humboldt, Trinity, Shasta, and Siskiyou) regions (Fig. 1). Moderate mean annual temperature (56.5 °F - 62.5 °F) and temperature anomaly (3.8 °F - 5.5 °F) were the most important variable predictor for high LD outbreak. …”
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“…Simulating the brain-body-environment trinity in closed loop is an attractive proposal to investigate how perception, motor activity and interactions with the environment shape brain activity, and vice versa. …”
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“…RESULTS: The ISPO lower-limb COMPASS resulted in the following 6 recommendations: (1) Amputee Mobility Predictor, Timed Up and Go, Two-Minute Walk Test, Prosthetic Evaluation Questionnaire—Residual Limb Health, Prosthetic Evaluation Questionnaire—Utility, and Trinity Amputation and Prosthesis Experience Scales-Revised, which make up the ISPO lower-limb COMPASS; (2) Comprehensive High-Level Activity Mobility Predictor and Six-Minute Walk Test are 2 additional outcome measures recommended for higher-activity-level individuals with LLA, which make up the COMPASS+; (3) Patient-Specific Function Scale makes up the COMPASS Adjunct; (4) a generic health-related quality of life outcome measure such as the European Quality of Life-5D-5L or Patient-Reported Outcomes Measurement Information System—29 item can be used to supplement the COMPASS; (5) outcome measures suited to low- and middle-income countries need to be developed with a focus on activities such as sitting cross-legged, kneeling, squatting, and other culturally important mobility-related activities; and (6) translation, validation, and open sharing of translated outcome measures included in the COMPASS, COMPASS+, and COMPASS Adjunct occurs. …”
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“…Hamer, MD, Kephera Diagnostics: Grant/Research Support|Takeda: Advisor/Consultant|Takeda: Grant/Research Support|Trinity Biotech, LLC: Advisor/Consultant|Valneva: Advisor/Consultant|Valneva: Grant/Research Support Natasha Hochberg, MD, MPH, Novartis Institute for Biomedical Research: Full-time employment|Novartis Institute for Biomedical Research: Stocks/Bonds Daniel Bourque, MD, Kephera Diagnostics: Grant/Research Support…”
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