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TRANSDECODER.LONGORFS(1) User Commands TRANSDECODER.LONGORFS(1)

NAME

TransDecoder.LongOrfs - extract long ORFs

DESCRIPTION

######################################################################################## # ______ ___ __ # /_ __/______ ____ ___ / _ \___ _______ ___/ /__ ____ # / / / __/ _ `/ _\(_-</ // / -_) __/ _ \/ _ / -_) __/ # /_/ /_/ \_,_/_//_/___/____/\__/\__/\___/\_,_/\__/_/ .LongOrfs # ######################################################################################## # # Transdecoder.LongOrfs|http://transdecoder.github.io> - Transcriptome Protein Prediction # # # Required: # # -t <string> transcripts.fasta # # Optional: # # --gene_trans_map <string> gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> ) # # -m <int> minimum protein length (default: 100) # # -S strand-specific (only analyzes top strand) # # --output_dir | -O <string> path to intended output directory # # --genetic_code | -G <string> genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia) # Genetic Codes (derived from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)# Acetabularia Candida Ciliate Dasycladacean Euplotid Hexamita Mesodinium Mitochondrial-Ascidian Mitochondrial-Chlorophycean Mitochondrial-Echinoderm Mitochondrial-Flatworm Mitochondrial-Invertebrates Mitochondrial-Protozoan Mitochondrial-Pterobranchia Mitochondrial-Scenedesmus_obliquus Mitochondrial-Thraustochytrium Mitochondrial-Trematode Mitochondrial-Vertebrates Mitochondrial-Yeast Pachysolen_tannophilus Peritrich SR1_Gracilibacteria Tetrahymena Universal # # --complete_orfs_only yields only complete ORFs (peps start with Met (M), end with stop (*)) # #########################################################################################

May 2026 TransDecoder.LongOrfs 6.0.0