ORFan is a suite of tools used for generating transcripts baring mutations or performing in-silico translation of cDNA sequences. It is written in Rust.
ORFan has 2 main functions:
- Generation of in-silico mutated transcripts
- Generation of in-silico mutated peptides
Usage: orfan transcript-mutator [OPTIONS] --vcf-file <vcf_file> --gtf-file <gtf_file> --reference-genome <reference_genome> --output-file <output_file>
Options:
-f, --vcf-file <vcf_file>
input vcf file containing mutations
-g, --gtf-file <gtf_file>
path to gtf annotation file
-r, --reference-genome <reference_genome>
reference genome in fasta format
-o, --output-file <output_file>
Path to output file
-s, --strand-aware-off
Whether to turn OFF strand aware sequence report. NOT RECOMMENDED TO BE TURNED OFF if the transcripts are going to be used to generate ORFs
-h, --help
Print help
-V, --version
Print versiontranscript-mutator requires you provide a vcf file containing coding mutations (mutations falling onto exonic regions), a gtf annotation file (can be found here), a reference genome in fasta format and an output file where to write the mutated transcripts.
Usage: orfan orf-seeker [OPTIONS] --input-file <input_fasta_file> --normal-fasta-file <normal_fasta_file> --output-file <output_fasta_file>
Options:
-i, --input-file <input_fasta_file>
Input fasta file
-n, --normal-fasta-file <normal_fasta_file>
Fasta file containing transcript sequences as obtained by seqtk
-o, --output-file <output_fasta_file>
Output fasta file
-m, --mutated-only
Whether to only write ORFs containing mutation
-l, --min-len <min_orf_len>
Minimum length of the ORF [default: 6]
-a, --all-codons
Whether to print ORFs starting with any codon
-w, --write-missing
Whether to write header line of missing ORFs in output
-h, --help
Print help
-V, --version
Print versionorf-seeker takes a set of transcripts and performs in-silico translation in all 3 frames. The output are peptide sequences. orf-seeker is based on tama-orf-seeker (PUT GITHUB PAGE).