(Q34356258)

1 August 2017

title

Assessing De Novo transcriptome assembly metrics for consistency and utility (English)

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1 August 2017

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2

Scott J Emrich

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1 August 2017

Shawn T O'Neil

1

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1 August 2017

language of work or name

English

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publication date

9 July 2013

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1 August 2017

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1 August 2017

volume

14

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1 August 2017

page(s)

465

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describes a project that uses

1 August 2017

MIRA

object named as

MIRA

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

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Transcriptomics in the RNA-seq era.

6 July 2018

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RNA-Seq Assembly - Are We There Yet?

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae).

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Performance comparison of benchtop high-throughput sequencing platforms

6 July 2018

1 reference

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Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

6 July 2018

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The head-regeneration transcriptome of the planarian Schmidtea mediterranea.

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Full-length transcriptome assembly from RNA-Seq data without a reference genome

6 July 2018

1 reference

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The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus.

6 July 2018

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Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Comparing de novo assemblers for 454 transcriptome data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Optimization of de novo transcriptome assembly from next-generation sequencing data

6 July 2018

1 reference

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A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

6 July 2018

1 reference

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Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

6 July 2018

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Modeling transcriptome based on transcript-sampling data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

What makes species unique? The contribution of proteins with obscure features

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

Choosing BLAST options for better detection of orthologs as reciprocal best hits.

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-14-465

Zipf's law in gene expression.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3733778

27 October 2018

Identifiers

DOI

10.1186/1471-2164-14-465

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Dimensions Publication ID

1 August 2017

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1 reference

1 August 2017

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