TRANSDECODER(1)

NAME
TransDecoder - full pipeline wrapper

DESCRIPTION
############################################################################################## # # TransDecoder - full pipeline wrapper # # Runs: LongOrfs -> [optional homology search] -> Predict -> [optional genome propagation] # # Input (choose one): # # -t|--transcripts <string> Transcripts FASTA file # # --genome <string> Genome FASTA file \ use together to extract # --gtf <string> Annotation GTF file / cDNA sequences via # gtf_genome_to_cdna_fasta.pl, then propagate # final ORFs back to genome coordinates. # # LongOrfs options: # # -m <int> Minimum protein length (default: 100) # -S Strand-specific (top strand only) # -G|--genetic_code <string> Genetic code (default: universal) # --gene_trans_map <string> Gene-to-transcript map (tab-delimited) # --complete_orfs_only Only report complete ORFs # # Homology search options: # # --blast_search_pep <string> Protein FASTA to search against; triggers # homology search (DB built automatically) # --blast_tool <string> 'diamond' or 'blastp' (default: diamond) # --blast_evalue <float> E-value cutoff (default: 1e-5) # --blast_threads <int> Threads for homology search (default: 1) # # Predict options: # # -T <int> Top ORFs for Markov model training (default: 500) # --retain_long_orfs_mode <string> 'dynamic' or 'strict' (default: dynamic) # --retain_long_orfs_length <int> Min length to auto-retain under strict mode # --pfam-search-db <string> Pfam HMM database to search with hmmsearch; # hmmpress is run automatically if needed # --single_best_only Retain only single best ORF per transcript # --no_refine_starts Skip start codon refinement # # Other: # # -O|--output_dir <string> Output directory (default: current directory) # -v|--verbose Verbose output # --version Show version and exit # ##############################################################################################