### Ropipe

    - Pipeline 1: download SRA and metadata
    
    - Pipeline 2 (RNAseq-related pipeline): Fastqc, MultiQC, Trinity, busco, kallisto and blastx

    - Pipeline 3 (sequence-based analyses): alignment, transcdecoder, revtrans, hmmcleaner, sequence renaming and preparation for Pelican sequence analyses, raxml-ng tree 


Pipeline 1 retrieve relevant rodent kidney public data

Pipeline 2 process RNAseq data including quality check, de novo assembly, quality estimation, quantification and transcript annotation using blastx against a curated EggNog library.

Output data from pipeline 2 are then used: 1- for expression analyses and 2- as input in pipeline 3 for gene alignment building.

Output data from pipeline 3 are then used: for detection of changes as input of Pelican
