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 release
Version 1.91 (2017-05-23)
  • Some external tools new version: bwa v0.7.15, samtools 1.3, Trinity 2.4.0, busco 3.0.
  • Add new normalization round after fastq merging for multi samples assemblies.
  • Parallelization of contig consensus editing.
  • Add busco graph to assessment report.
  • Fix various bugs.
  • Update Docker image.
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)