This repository contains a collection of scripts used to do the "Inference and functional annotation of the sugarcane pantranscriptome". Read more about the project: https://bv.fapesp.br/en/bolsas/190447/inference-and-annotation-of-the-sugarcane-pantranscriptome/

This figure represents the almost complete collection of messenger RNA produced by a specie (Saccharum hybrid cultivar in this study). This collection can be called as pantranscriptome. The pantranscriptome of a specie can allow us to make coss-cultivar comparisons as well as to explore co-expression networks that will in turn aid in the functional annotation of until then transcripts of unknown function.

Contact information:

Prof. Dr. Diego Mauricio Riaño-Pachón: diego.riano@cena.usp.br

Felipe Vaz Peres: felipe.vzps@gmail.com

• MyAssembly_Template
  • Template used to assembly transcriptomes from their raw RNAseq datasets.
• Scripts
  • extract_contaminants.py: Script to extract and count the total reads of contaminant organisms based in the Kaiju report.
  • Snakefile: configuration file of our pipeline to semi-automatically generate sugarcane de novo transcriptome assemblies and remove possible genetic material from contaminant organisms in the reads.

This research has been supported by São Paulo Research Foundation (FAPESP), process number: 19/24796-5 and by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), process number: 310080/2018-5