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Santiago Montero-Mendieta edited this page May 19, 2017 · 72 revisions

PRACTICAL GUIDE TO BUILD DE-NOVO TRANSCRIPTOME ASSEMBLIES FOR NON-MODEL ORGANISMS

This is a simple workflow to assist the inexperienced user with pre-processing, assembling and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. In order to successfully run all the steps, we recommend to use a linux computer with at least 8 cores. Please consider adapting file names and paths for your own use. For any inquiry, please contact: santiago.montero@ebd.csic.es

Guide Overview

1. Software and data required

2. Quality control using FASTQC

3. Ribosomal RNA removal using SORTMERNA

4. Quality trimming and adapter removal using TRIMMOMATIC

5. Normalization using TRINITY

6. De-novo transcriptome assembly using TRINITY

7. Assembly validation using BOWTIE, BUSCO & BLASTX

8. Functional annotation using TRINOTATE


Citation

Montero-Mendieta S, Grabherr M, Lantz H, De la Riva I, Leonard JA, Webster MT, Vilà C. (2017) First de-novo transcriptome assembly of a South American frog, Oreobates cruralis, enables population genomic studies of Neotropical amphibians. PeerJ Preprints 5:e2980v1 https://doi.org/10.7287/peerj.preprints.2980v1