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 sever...
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PeerJ Inc.
2017-02-01
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| Online Access: | https://peerj.com/articles/2988.pdf |
| _version_ | 1797418386076991488 |
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| author | Cédric Cabau Frédéric Escudié Anis Djari Yann Guiguen Julien Bobe Christophe Klopp |
| author_facet | Cédric Cabau Frédéric Escudié Anis Djari Yann Guiguen Julien Bobe Christophe Klopp |
| author_sort | Cédric Cabau |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T06:33:01Z |
| format | Article |
| id | doaj.art-6f05f9f61036480b81de3015a0d071a3 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:33:01Z |
| publishDate | 2017-02-01 |
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| series | PeerJ |
| spelling | doaj.art-6f05f9f61036480b81de3015a0d071a32023-12-03T11:02:52ZengPeerJ Inc.PeerJ2167-83592017-02-015e298810.7717/peerj.2988Compacting and correcting Trinity and Oases RNA-Seq de novo assembliesCédric Cabau0Frédéric Escudié1Anis Djari2Yann Guiguen3Julien Bobe4Christophe Klopp5SIGENAE, GenPhySE, Université de Toulouse, INRA, INPT, ENV, Castanet Tolosan, FrancePlate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet Tolosan, FranceLaboratoire Génomique et Biotechnologie du Fruit, UMR990 INRA/INP-ENSAT, Auzeville, FranceUR1037 Fish Physiology and Genomics, INRA, Rennes, FranceUR1037 Fish Physiology and Genomics, INRA, Rennes, FranceSIGENAE, GenPhySE, Université de Toulouse, INRA, INPT, ENV, Castanet Tolosan, FranceBackground 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.https://peerj.com/articles/2988.pdfRNA-SeqDe novo assemblyCompactionCorrectionQuality assessment |
| spellingShingle | Cédric Cabau Frédéric Escudié Anis Djari Yann Guiguen Julien Bobe Christophe Klopp Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies PeerJ RNA-Seq De novo assembly Compaction Correction Quality assessment |
| title | Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies |
| title_full | Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies |
| title_fullStr | Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies |
| title_full_unstemmed | Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies |
| title_short | Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies |
| title_sort | compacting and correcting trinity and oases rna seq de novo assemblies |
| topic | RNA-Seq De novo assembly Compaction Correction Quality assessment |
| url | https://peerj.com/articles/2988.pdf |
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