TRUFA (Transcriptomes User-Friendly Analysis) is a free webserver designed to help you perform RNA-seq analysis.

So far, TRUFA is allowing you to execute the following steps (programs used are specified in the parentheses):

Reads cleaning:
Reads quality control (FASTQC)
Quality trimming and duplicates removal (Prinseq)
Trimming adapters (Cutadapt)
Filtering out potential contaminants (Blat)
De novo assembly of your reads (Trinity)
Reads mapping (Bowtie2)
Contigs (i.e transcripts) identification based on:
sequence alignment (Blat, Blast)
protein dominions, profiles (HMMER)
Annotation with GO terms (Blast2GO)
Expression quantification: providing TPMs, FPKMs and read counts (RSEM, eXpress)

https://trufa.ifca.es/web/

Keywords: RNA-seq

Authors: Kornobis, Cabellos, Aguilar, Frias-Lopez, Rozas, Marco & Zardoya

Scientific topics: Regulatory RNA