Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.

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Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

10.7287/peerj.preprints.2284 ◽

2016 ◽

Author(s):

Cédric Cabau ◽

Frédéric Escudié ◽

Anis Djari ◽

Yann Guiguen ◽

Julien Bobe ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Error Rates ◽

Rna Seq ◽

De Novo Transcriptome ◽

Software Packages ◽

Redundancy Reduction ◽

Assembly Pipeline ◽

Free Open Source

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .

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Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

10.7287/peerj.preprints.2284v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Cédric Cabau ◽

Frédéric Escudié ◽

Anis Djari ◽

Yann Guiguen ◽

Julien Bobe ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Error Rates ◽

Rna Seq ◽

De Novo Transcriptome ◽

Software Packages ◽

Redundancy Reduction ◽

Assembly Pipeline ◽

Free Open Source

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .

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The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras

10.1101/495754 ◽

2018 ◽

Author(s):

Jesse Kerkvliet ◽

Arthur de Fouchier ◽

Michiel van Wijk ◽

Astrid T. Groot

Keyword(s):

Quality Control ◽

Quality Assessment ◽

Reference Genome ◽

Assessment Tool ◽

De Novo ◽

Transcriptome Assembly ◽

Rna Seq ◽

Quality Assessment Tool ◽

Chimeric Sequences

AbstractTranscriptome quality control is an important step in RNA-seq experiments. However, the quality of de novo assembled transcriptomes is difficult to assess, due to the lack of reference genome to compare the assembly to. We developed a method to assess and improve the quality of de novo assembled transcriptomes by focusing on the removal of chimeric sequences. These chimeric sequences can be the result of faulty assembled contigs, merging two transcripts into one. The developed method is incorporated into a pipeline, that we named Bellerophon, which is broadly applicable and easy to use. Bellerophon first uses the quality-assessment tool TransRate to indicate the quality, after which it uses a Transcripts Per Million (TPM) filter to remove lowly expressed contigs and CD-HIT-EST to remove highly identical contigs. To validate the quality of this method, we performed three benchmark experiments: 1) a computational creation of chimeras, 2) identification of chimeric contigs in a transcriptome assembly, 3) a simulated RNAseq experiment using a known reference transcriptome. Overall, the Bellerophon pipeline was able to remove between 40 to 91.9% of the chimeras in transcriptome assemblies and removed more chimeric than non-chimeric contigs. Thus, the Bellerophon sequence of filtration steps is a broadly applicable solution to improve transcriptome assemblies.

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A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

PeerJ ◽

10.7717/peerj.3702 ◽

2017 ◽

Vol 5 ◽

pp. e3702 ◽

Cited By ~ 5

Author(s):

Santiago Montero-Mendieta ◽

Manfred Grabherr ◽

Henrik Lantz ◽

Ignacio De la Riva ◽

Jennifer A. Leonard ◽

...

Keyword(s):

Defense Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Cost Effective ◽

Model Organisms ◽

Rna Seq ◽

Assembly Pipeline ◽

Wide Variability ◽

History Of ◽

Inexperienced User

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembledde-novo. We used RNA-seq to obtain the transcriptomic profile forOreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome ofO. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating ade-novotranscriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to buildde-novotranscriptome assemblies using readily available software and is freely available at:https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

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Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

BMC Genomics ◽

10.1186/1471-2164-11-663 ◽

2010 ◽

Vol 11 (1) ◽

pp. 663 ◽

Cited By ~ 151

Author(s):

Jeffrey Martin ◽

Vincent M Bruno ◽

Zhide Fang ◽

Xiandong Meng ◽

Matthew Blow ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

De Novo Transcriptome Assembly ◽

Rna Seq ◽

De Novo Transcriptome ◽

Assembly Pipeline

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Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species

10.7287/peerj.preprints.505 ◽

2014 ◽

Cited By ~ 2

Author(s):

Elijah K Lowe ◽

Billie J Swalla ◽

C. Titus Brown

Keyword(s):

Developmental Stages ◽

De Novo ◽

Transcriptome Assembly ◽

Marine Species ◽

Model Organisms ◽

The Past ◽

Ascidian Species ◽

Assembly Pipeline ◽

Quality Filtering

De novo transcriptome sequencing and assembly for non-model organisms has become prevalent in the past decade. However, most assembly approaches are computationally expensive, and little in-depth evaluation has been done to compare de novo approaches. We sequenced several developmental stages of two free-spawning marine species—Molgula occulta and Molgula oculata—assembled their transcriptomes using four different combinations of preprocessing and assembly approaches, and evaluated the quality of the assembly. We present a straightforward and reproducible mRNAseq assembly protocol that combines quality filtering, digital normalization, and assembly, together with several metrics to evaluate our de novo assemblies. The use of digital normalization in the protocol reduces the time and memory needed to complete the assembly and makes this pipeline available to labs without large computing infrastructure. Despite varying widely in basic assembly statistics, all of the assembled transcriptomes evaluate well in metrics such as gene recovery and estimated completeness.

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Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species

10.7287/peerj.preprints.505v1 ◽

2014 ◽

Cited By ~ 6

Author(s):

Elijah K Lowe ◽

Billie J Swalla ◽

C. Titus Brown

Keyword(s):

Developmental Stages ◽

De Novo ◽

Transcriptome Assembly ◽

Marine Species ◽

Model Organisms ◽

The Past ◽

Ascidian Species ◽

Assembly Pipeline ◽

Quality Filtering

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Comprehensive transcriptome analysis of grafting onto Artemisia scoparia W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

10.21203/rs.2.10583/v2 ◽

2019 ◽

Author(s):

Xue-ying Zhang(Former Corresponding Author) ◽

Xian-zhi Sun(New Corresponding Author) ◽

Sheng Zhang ◽

Fang-fang Liu ◽

Jing-hui Yang ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Chrysanthemum Morifolium ◽

De Novo Transcriptome Assembly ◽

Rna Seq ◽

De Novo Transcriptome ◽

Biotic And Abiotic Stresses ◽

Yield And Quality ◽

Artemisia Scoparia

Abstract Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self - rooted grafted chrysanthemum ( Chrysanthemum morifolium 'Hangbaiju') and the grafted Artermisia-chrysanthemum ( grafted onto Artemisia scoparia ) transcription response to aphid stress.

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