de novo assembly of a transcriptome from juvenile blue

Characterization of a de novo assembled transcriptome of

De novo assembly and annotation of the transcriptome and alignment of the reads. For the de novo assembly of the transcriptome and the single tissues the assembling tools Velvet 1.2.10 (Zerbino & Birney, 2008) and Oases 0.2.08 (Schulz et al., 2012) were used. Before starting the assembly, the two PE files of each individual had to be shuffled

Combined de novo and genome guided assembly and

Transcriptome assembly Multiple k-mer de novo transcriptome assembly De novo transcriptome assembly was performed using three assemblers; Trinity r2013-11-10 [22], SOAPdenovo-Trans v1.04 [23] and Velvet v1.2.10/ Oases v0.2.08 [24, 25]. Assembly with Trinity was performed on both data-sets using default parameters [26], except min_conti- De Novo Assembly and Annotation of the Juvenile Tuber Gastrodia elata is a traditional Chinese herbal medicine with good therapeutic effect on various nervous and cerebrovascular diseases. In the present study, we generated 20,611,556 raw reads from the young tuber transcriptome of a G. elata hybrid (Gastrodia elata BI.f.elata × Gastrodia elata BI.f.pilifera) by using Illumina HiSeq 4000 sequencing platform. De novo assembly and

De Novo Assembly and Annotation of the Juvenile Tuber

Gastrodia elata is a traditional Chinese herbal medicine with good therapeutic effect on various nervous and cerebrovascular diseases. In the present study, we generated 20,611,556 raw reads from the young tuber transcriptome of a G. elata hybrid (Gastrodia elata BI.f.elata × Gastrodia elata BI.f.pilifera) by using Illumina HiSeq 4000 sequencing platform. De novo assembly and De Novo Assembly and Characterization of the Transcriptome De Novo Assembly, Refinement, and Quality Assessment of the Dodder Transcriptome. In organisms without a reference genome, massive Illumina short-read sequencing, in conjunction with efficient de novo transcriptome assembly, has become a feasible method for generating a reference transcriptome with sufficient depth coverage to carry out differential gene eion analysis (Wang

De Novo Assembly and Characterization of the Transcriptome

De Novo Assembly, Refinement, and Quality Assessment of the Dodder Transcriptome. In organisms without a reference genome, massive Illumina short-read sequencing, in conjunction with efficient de novo transcriptome assembly, has become a feasible method for generating a reference transcriptome with sufficient depth coverage to carry out differential gene eion analysis (Wang De Novo Assembly of the Transcriptome of Turritopsis, a Aug 01, 2016 · De novo transcriptome assembly and annotation Prior to assembly, adapter sequences were removed from raw reads, and the trimmed reads were assessed for quality using FASTX Toolkit (v0.0.13) software. Base trimming was done from the 3 end of each read to remove bases with a quality below Q10 up to a minimum length of 50 bp. Reads shorter than

De Novo Sequencing and Transcriptome Analysis of the

Aug 01, 2012 · In contrast, OASES, Trinity and Rnnotator were developed as de novo transcriptome assemblers with a strategy that merges the contigs obtained by the first assembly. It is also consistent with the previous report that Velvet itself is not sufficient for assembly of long contigs in de novo transcriptome sequencing with an Illumina Genome Analyzer . De novo Transcriptome Analysis of Portunus trituberculatus Jun 04, 2015 · The de novo transcriptome assembly performed with Trinity using both ovary and testis reads (128,904,126 reads in all) generated a total of 80,527 transcripts. The length distribution of the assembled transcripts is as shown in S1 Fig .

De novo assembly and characterization of farmed blue fox

The blue fox (Alopex lagopus), a coat-color variant of the Arctic fox, is a domesticated fur-bearing mammal. In the present study, transcriptome data generated from a pool of nine different tissues were obtained with Illumina HiSeq2500 paired-end sequencing technology. After filtering from raw reads, 32,358,290 clean reads were assembled into 161,269 transcripts and 97,252 unigenes by the De novo assembly and characterization of farmed blue fox The blue fox (Alopex lagopus), a coat-color variant of the Arctic fox, is a domesticated fur-bearing mammal. In the present study, transcriptome data generated from a pool of nine different tissues were obtained with Illumina HiSeq2500 paired-end sequencing technology. After filtering from raw reads, 32,358,290 clean reads were assembled into 161,269 transcripts and 97,252 unigenes by the

De novo assembly and functional annotation of the olive

De novo assembly and functional annotation of the olive (Olea europaea) transcriptome. Muñoz-Mérida A(1), González-Plaza JJ, Cañada A, Blanco AM, García-López Mdel C, Rodríguez JM, Pedrola L, Sicardo MD, Hernández ML, De la Rosa R, Belaj A, Gil-Borja M, Luque F, Martínez-Rivas JM, Pisano DG, Trelles O, Valpuesta V, Beuzón CR. De novo assembly of a transcriptome from juvenile blue De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil Article (PDF Available) in BMC Genomics 16

De novo assembly of a transcriptome from juvenile blue

De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus)following exposure to surrogate Macondo crude oil Bree K. Yednock1*, Timothy J. Sullivan2 and Joseph E. Neigel2 De novo assembly of a transcriptome from juvenile blue Jan 01, 2015 · De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil.

De novo assembly of a transcriptome from juvenile blue

Jul 11, 2015 · Yednock, B.K., Sullivan, T.J. & Neigel, J.E. De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil. BMC Genomics 16, 521 (2015). https://doi/10.1186/s12864-015-1739-2. Download citation. Received:13 January 2015. Accepted:29 June 2015 De novo assembly of a transcriptome from juvenile blue Yednock et al. BMC Genomics De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil Bree K. Yednock 1 Timothy J. Sullivan 0 Joseph E. Neigel 0 0 Department of Biology, University of Louisiana at Lafayette , Lafayette, LA , USA 1 South Slough National Estuarine Research Reserve , Charleston, OR , USA Background:The blue crab, Callinectes sapidus

De novo assembly transcriptome analysis reveals the

Sep 01, 2020 · De novo transcriptome sequencing, assembly, and gene function annotation Nine cDNA libraries were constructed from three hard clam juvenile groups (NP, W, and OP), with three replicates per group. A total of 61.28 Gb of raw data were obtained after Illumina sequencing and deposited in the NCBI SRA database under accession number (PRJNA598374). De novo transcriptome assembly and data for the blue Jun 01, 2020 · De novo transcriptome assembly was completed using Trinity with default options and requiring a minimum contig length of 200 nt. Clustering of similar transcripts was performed using CD-HIT-EST [8,9] and transcript were quality filtered using TransRate . This filtered transcriptome contained 571,105 transcripts associated with 449,956 unigenes.

De novo transcriptome assembly, annotation and

Jan 08, 2018 · Improved de novo assembly methods enable robust generation of a reference transcriptome and offer an important alternative to genome reference mapping [28,29,30]. Thus data generated as part of small-scale projects, such as the four species transcriptome resources presented in the current study, provide a valuable contribution to the De novo transcriptome assembly, functional De novo transcriptome assembly, functional annotation and differential gene eion analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies Michelle Thunders 1*, Jo Cavanagh2 and Yinsheng Li3 Abstract

De novo transcriptome assembly, functional annotation

Feb 27, 2017 · De novo transcriptome assembly. Trinity is a freely available software tool used for de novo transcriptome assembly that uses three software modules (Inchworm, Chrysalis and Butterfly) to assemble a de novo transcriptome when no model data is available [], it does this by first assembling the RNA sequence data into transcripts or genes, clustering these contigs, constructing de Bruijn De novo transcriptome assembly, functional annotation Feb 27, 2017 · De novo transcriptome assembly. Trinity is a freely available software tool used for de novo transcriptome assembly that uses three software modules (Inchworm, Chrysalis and Butterfly) to assemble a de novo transcriptome when no model data is available [], it does this by first assembling the RNA sequence data into transcripts or genes, clustering these contigs, constructing de Bruijn

De novo transcriptome assembly, functional annotation

Results. This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool. Trinotate was used to carry out functional annotation of the Trinity generated transcriptome file and the transdecoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 database. De novo transcriptome of Ischnura elegans provides Here, we present a comprehensive de novo transcriptome assembly for the blue-tailed damselfly Ischnura elegans (Odonata:Coenagrionidae) built from short-read RNA-seq data. The transcriptome analysis in this paper provides a first step towards identifying genes and pathways underlying the visual and colour systems in this insect group.

Evaluation of de novo transcriptome assemblies from RNA

Dec 21, 2014 · De novo RNA-Seq assembly facilitates the study of transcriptomes for species without sequenced genomes, but it is challenging to select the most accurate assembly in this context. To address this challenge, we developed a model-based score, RSEM-EVAL, for evaluating assemblies when the ground truth is unknown. We show that RSEM-EVAL correctly reflects assembly accuracy, IDP-denovo:de novo transcriptome assembly and isoform Without a reference genome, IDP-denovo performs de novo transcriptome assembly, isoform annotation and quantification by integrating the strengths of LRs and short reads. Using the GM12878 human data as a gold standard, we demonstrated that IDP-denovo had superior sensitivity of transcript assembly and high accuracy of isoform annotation.

Next-generation transcriptome assembly

However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches reference-based, de novo and combined strategies Next-generation transcriptome assemblyHowever, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches reference-based, de novo and combined strategies

Study Provides 1st Large-Scale Blue Crab Transcriptome

The authors published their findings in BMC Genomics:De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil. The Deepwater Horizon spill contaminated northern Gulf of Mexico marsh habitats with dispersed crude oil where the blue crab ( Callinectes sapidus ) , an economically important species that supports a The Oyster River Protocol:a multi-assembler and kmer Given this, the production of a de novo transcriptome assembly requires a large investment in time and resources, with each step requiring careful consideration. Here, I propose an evidence-based protocol for assembly that results in the production of high quality transcriptome assemblies, across a variety of commonplace experimental conditions

The Oyster River Protocol:a multi-assembler and kmer

Given this, the production of a de novo transcriptome assembly requires a large investment in time and resources, with each step requiring careful consideration. Here, I propose an evidence-based protocol for assembly that results in the production of high quality transcriptome assemblies, across a variety of commonplace experimental conditions The Tomato Translational Landscape Revealed by Next, we performed reference-guided de novo transcriptome assembly for the RNA-seq data using stringtie, a transcript assembler (Pertea et al., 2015). Then, the newly assembled transcriptomes from the replicates were merged and compared with the ITAG3.2 annotations using gffcompare software ( Pertea et al., 2016 ; Fig. 1C ).

Transcriptome assembly from long-read RNA-seq

Dec 16, 2019 · Transcriptome assembly of short RNA-seq reads. We first used simulated human data to compare the sensitivity and precision of StringTie2, with and without super-reads, to that of Scallop (Fig. 1), one of the most recent transcriptome assemblers for short RNA-seq data, which was shown on some data to yield an improvement in assembly accuracy over StringTie1 []. rnaSPAdes:a de novo transcriptome assembler and its The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes.

rnaSPAdes:a de novo transcriptome assembler and its

The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo assembly of a transcriptome from juvenile blue De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil Bree K. Yednock , Timothy J. Sullivan , and Joseph E. Neigel South Slough National Estuarine Research Reserve, Charleston, OR USA