├── Installation_notes.md ├── LICENSE ├── Project_Carbonate_v4 ├── README ├── SOAP │ ├── Combine.sh │ ├── README │ ├── RunSOAP1.sh │ ├── RunSOAP1b.sh │ └── config_file ├── Setup.ba ├── TransAbyss │ ├── Combine.sh │ ├── README │ ├── RunTransAb1.sh │ └── RunTransAb1b.sh ├── Trinity │ ├── README │ └── RunTrinity.sh ├── Velvet │ ├── Combine.sh │ ├── README │ ├── RunVelvet1.sh │ ├── RunVelvet1b.sh │ ├── RunVelvet2.sh │ ├── RunVelvet2b.sh │ ├── RunVelvet3.sh │ └── RunVelvet3b.sh ├── final_assemblies │ ├── Combine.sh │ ├── DE │ │ ├── README │ │ └── adjust_matrix.sh │ ├── QC │ │ ├── README │ │ └── RunQC.sh │ ├── README │ ├── RunEviGene.sh │ ├── annotation │ │ ├── Annotate.sh │ │ ├── README │ │ ├── RunAnnotate.sh │ │ ├── RunTrinotate.sh │ │ └── scripts │ │ │ ├── convert_aa.ba │ │ │ ├── make_genes_to_transcripts.ba │ │ │ └── subset_fasta.pl │ └── backwards_compatibility │ │ └── README ├── input_files │ ├── README │ └── RunTrinity.normalize.sh └── setup_files │ ├── citations │ ├── paired2single │ 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