A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. (Q34622085)

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26 February 2020

title

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly (English)

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26 February 2020

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1

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26 February 2020

Rainer Kiko

3

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26 February 2020

author name string

Lynne M Christianson

2

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26 February 2020

Meghan L Powers

4

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26 February 2020

Nathan C Shaner

5

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26 February 2020

Steven H D Haddock

6

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26 February 2020

language of work or name

English

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publication date

12 March 2013

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26 February 2020

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26 February 2020

volume

14

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26 February 2020

page(s)

167

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Annotation of the transcriptome from Taenia pisiformis and its comparative analysis with three Taeniidae species

26 February 2020

cites work

1 reference

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Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

7 July 2018

1 reference

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Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

7 July 2018

1 reference

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Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus

7 July 2018

1 reference

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De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes

7 July 2018

1 reference

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Differential expression in RNA-seq: a matter of depth

7 July 2018

1 reference

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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

7 July 2018

1 reference

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

7 July 2018

1 reference

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Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds.

7 July 2018

1 reference

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De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification

7 July 2018

1 reference

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De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

De novo characterization of a whitefly transcriptome and analysis of its gene expression during development.

7 July 2018

1 reference

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Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

7 July 2018

1 reference

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BLAST+: architecture and applications

7 July 2018

1 reference

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Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

Assessing the gene space in draft genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

RNA-Seq: a revolutionary tool for transcriptomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

Stem cell transcriptome profiling via massive-scale mRNA sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

7 July 2018

1 reference

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The COG database: an updated version includes eukaryotes

7 July 2018

1 reference

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Initial sequencing and comparative analysis of the mouse genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

7 July 2018

1 reference

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Beware of mis-assembled genomes.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655071

An analysis on gene architecture in human and mouse genomes.

26 October 2018

1 reference

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26 October 2018

Identifiers

DOI

10.1186/1471-2164-14-167

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26 February 2020

1 reference

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26 February 2020

1 reference

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