De novo RNA-seq Assembly Pipeline

Short read RNASeq de novo assembly is a well established method to study transcription of organisms lacking a reference genome sequence. Available software packages such as Trinity and Oases have proven to be able to build high quality contigs from short reads. But there is still room for improvement on different points such as:

DRAP includes three modules:

Last releases
Version 1.9 (2016-12-19)
  • Docker image is now available.
  • Read normalization can be run using Trinity or Khmer.
  • Parallelization of multi sample assemblies processing.
  • Parallelization of local (non SGE) assemblies processing.
  • TSA checking now includes vector/adaptor and contaminants detection.
  • New embedded Trinity version is the last production version i.e. v2.3.
  • New embedded BUSCO version is 2.0.
Version 1.8 (2016-05-20)
  • Add BUSCO in runAssessment procedure.
Version 1.7 (2015-09-25)
  • Add runAssessment to evaluate assemblies.
  • Add runCheck to check the workflows dependencies.
  • Add assembly scoring by TransRate
Citation
Cabau C, EscudiƩ F, Djari A, Guiguen Y, Bobe J, Klopp C. (2017)
Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ 5:e2988.
https://doi.org/10.7717/peerj.2988
License
GNU GPLv3 (details)