Santiago Montero-Mendieta edited this page Sep 5, 2016 · 50 revisions

Quick Guide to Build De-novo Assemblies

This is a pipeline that you can use to pre-process, reconstruct and analyze de-novo transcriptome assemblies using RNA-Seq data. Please consider adapting file names and paths for your own use. For any inquiry, please contact me: santiago.montero@ebd.csic.es

Pipeline Overview

  1. Get your RNA-Seq data

  2. Quality control (FastQC)

  3. rRNA removal (SortMeRNA)

  4. Quality trimming & adapter removal (Trimmomatic)

  5. Quality control (FastQC) (again)

  6. Normalize data (Trinity)

  7. Merge data (only when you have multiple tissues per sample, if not, go to step 9)

  8. Normalize data (Trinity) (again)

  9. De-novo assembly (Trinity)

  10. Gene annotation (Trinotate)


Montero-Mendieta, S. (2016): Quick guide to build de-novo assemblies. Available at: https://github.com/biomendi/QUICK-GUIDE-TO-BUILD-DE-NOVO-ASSEMBLIES/wiki