Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue PeerJ Année : 2017

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

Résumé

Background - Results - We built a 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 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.
Fichier principal
Vignette du fichier
Cabau_2016_PeerJ_{1632F66F-F563-45F4-AA17-F525DAE0C308}.pdf (998.53 Ko) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)
Loading...

Dates et versions

hal-01506620 , version 1 (12-04-2017)

Licence

Paternité

Identifiants

Citer

Cédric Cabau, Frédéric Escudie, Anis Djari, Yann Guiguen, Julien Bobe, et al.. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ, 2017, 5, pp.e2988. ⟨10.7717/peerj.2988⟩. ⟨hal-01506620⟩
164 Consultations
193 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More