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trinity software  (Illumina Inc)


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    Structured Review

    Illumina Inc trinity software
    Trinity Software, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/trinity+software/trinity+software/pmc12116482-77-5-13
    Average 90 stars, based on 1 article reviews
    trinity software - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Software:

    Article Title: RNA-Seq Analysis of Aboveground and Underground Parts of Biomass Sorghum Was Performed to Evaluate Its Suitability for Environmental Remediation
    Article Snippet: After the total RNA was checked, the library was constructed and sequenced by Gene Denovo Biotechnology Co. (Guangzhou, China) using an Illumina HiSeq2500. .. High-quality and valid data filtered from the samples were mixed and spliced using Trinity software (Illumina, San Diego, CA, USA, accessed on 5 January 2022) [ ], and various information from the obtained transcript was counted. .. Unigene sequences were compared to NR (non-redundant), PFAM (protein families), Swiss-Prot ( www.expasy.ch/sprot/ , accessed on 5 January 2022), and KEGG (Kyoto) by BLASTx.

    Article Title: Multiple bHLH/MYB-based protein complexes regulate proanthocyanidin biosynthesis in the herbage of Lotus spp.
    Article Snippet: Then the ratio of Firefly luciferase to Renilla luciferase fluorescence was measured using DualGlo® Luciferase Assay System (Promega) on a luminometer (Luminoskan Ascent, Thermo Scientific). .. Illumina Hiseq 1500 sequencing, de novo assembly of L. corniculatus and L. tenuis transcriptomes and functional annotation After adapter sequences were trimmed and sequences shorter than 90 bases removed, 200,136,278 and 181,191,352 clean paired-end reads remained for de novo assembly by Trinity software. ..

    Article Title: The short-term effect of nitrogen and phosphorus fertilizers on cold resistance in Urtica cannabina based on transcriptomics and metabolomics analysis
    Article Snippet: .. Transcriptome assembly was performed using Trinity software (version 2.13.2) using both the cleaned Illumina short reads and Nanopore long reads by implementing the long-reads flag. ..

    Article Title: RNA-Seq Analysis of Aboveground and Underground Parts of Biomass Sorghum Was Performed to Evaluate Its Suitability for Environmental Remediation.
    Article Snippet: After the total RNA was checked, the library was constructed and sequenced by Gene Denovo Biotechnology Co. (Guangzhou, China) using an Illumina HiSeq2500. .. High-quality and valid data filtered from the samples were mixed and spliced using Trinity software (Illumina, San Diego, CA, USA, accessed on 5 January 2022) [33], and various information from the obtained transcript was counted. .. Unigene sequences were compared to NR (non-redundant), PFAM (protein families), Swiss-Prot (www.expasy.ch/sprot/, accessed on 5 January 2022), and KEGG (Kyoto) by BLASTx.

    Article Title: Transcriptome Responses to Different Environments in Intertidal Zones in the Peanut Worm Sipunculus nudus .
    Article Snippet: .. Trinity software parameters were as follows: min kmer cov = 4, group pairs distance = 500, and the software was employed for the Illumina short-read assembly, which involved merging and extending the clean reads into longer fragments and transcripts. ..

    Article Title: Enhancing transcriptome analysis in medicinal plants: multiple unigene sets in Astragalus membranaceus .
    Article Snippet: Set-2 consisted of hybridized assembled unigenes with Illumina sequencing (Illumina-seq) reads and PacBio CCS using rnaSPAdes. .. Set-3 unigenes were assembled from Illumina-seq reads using the Trinity software. .. Construction of multiple unigene sets provides several advantages for transcriptome analysis.

    Article Title: Simple Sequence Repeats (SSRs) and Telomeric Analysis in Somatic Organs of Reproductive and Non-Reproductive Castes of Termite Reticulitermes chinensis
    Article Snippet: .. Sequence reads were annotated using the Illumina HiSeqTM 4000 platform and Trinity software (trinityrnaseq r2012-04-27), encompassing a diverse range of base pair (bp) lengths derived from transcriptome data [ ]. ..

    Article Title: Identification of the Mitf gene mutation causing congenital deafness and pigmentation disorders in porcupines using BSA-Seq
    Article Snippet: .. Using Trinity software, the gold standard for assembling Illumina short-read sequences, we constructed reference sequences from clean reads. ..

    Sequencing:

    Article Title: Multiple bHLH/MYB-based protein complexes regulate proanthocyanidin biosynthesis in the herbage of Lotus spp.
    Article Snippet: Then the ratio of Firefly luciferase to Renilla luciferase fluorescence was measured using DualGlo® Luciferase Assay System (Promega) on a luminometer (Luminoskan Ascent, Thermo Scientific). .. Illumina Hiseq 1500 sequencing, de novo assembly of L. corniculatus and L. tenuis transcriptomes and functional annotation After adapter sequences were trimmed and sequences shorter than 90 bases removed, 200,136,278 and 181,191,352 clean paired-end reads remained for de novo assembly by Trinity software. ..

    Article Title: Simple Sequence Repeats (SSRs) and Telomeric Analysis in Somatic Organs of Reproductive and Non-Reproductive Castes of Termite Reticulitermes chinensis
    Article Snippet: .. Sequence reads were annotated using the Illumina HiSeqTM 4000 platform and Trinity software (trinityrnaseq r2012-04-27), encompassing a diverse range of base pair (bp) lengths derived from transcriptome data [ ]. ..

    Functional Assay:

    Article Title: Multiple bHLH/MYB-based protein complexes regulate proanthocyanidin biosynthesis in the herbage of Lotus spp.
    Article Snippet: Then the ratio of Firefly luciferase to Renilla luciferase fluorescence was measured using DualGlo® Luciferase Assay System (Promega) on a luminometer (Luminoskan Ascent, Thermo Scientific). .. Illumina Hiseq 1500 sequencing, de novo assembly of L. corniculatus and L. tenuis transcriptomes and functional annotation After adapter sequences were trimmed and sequences shorter than 90 bases removed, 200,136,278 and 181,191,352 clean paired-end reads remained for de novo assembly by Trinity software. ..

    Derivative Assay:

    Article Title: Simple Sequence Repeats (SSRs) and Telomeric Analysis in Somatic Organs of Reproductive and Non-Reproductive Castes of Termite Reticulitermes chinensis
    Article Snippet: .. Sequence reads were annotated using the Illumina HiSeqTM 4000 platform and Trinity software (trinityrnaseq r2012-04-27), encompassing a diverse range of base pair (bp) lengths derived from transcriptome data [ ]. ..

    Construct:

    Article Title: Identification of the Mitf gene mutation causing congenital deafness and pigmentation disorders in porcupines using BSA-Seq
    Article Snippet: .. Using Trinity software, the gold standard for assembling Illumina short-read sequences, we constructed reference sequences from clean reads. ..



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