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-h, --help
Shows the help and exits.
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--codon-table
Codon table ID to be used for the considered chromosomes.
The ID must be consistent with the NCBI codon table IDs (see
NCBI Codon Tables).
(Default: The standard codon table, ID = 1).
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--chr
List of seqID to be treated by ORFtrack (i.e., column #1 of the GFF file, generally chromosome or contig ID).
IDs must be separated by a space:
--chr NC_001148.4 NC_001139.3
In this case, ORFtrack will not treat the entire genome but only the specified seqIDs.
Recommendation: Use this option for large genomes to distribute calculations across multiple CPUs.
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--chr-exclude
List of seqID(s) to exclude from processing.
(Default: None).
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--types_only
Genomic feature(s) considered for the annotation step (CDS is included by default).
If multiple genomic features are considered, they must be separated by spaces.
Noncoding ORFs are annotated as intergenic (if they do not overlap any feature) or overlapping (if they overlap a given genomic feature).
(See the ORFget section for more details).
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--types_except
Genomic feature(s) excluded from the annotation step (gene and exon are excluded by default).
If multiple genomic features are excluded, they must be separated by spaces.
Noncoding ORFs will be annotated as intergenic or overlapping another feature not listed here.
(See the ORFget section for more details).
-
--orf_len
Minimal number of nucleotides between two consecutive STOP codons to define an ORF.
(Default: 60 nucleotides).
(See the ORF definition section for more details).
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--co_ovp
Minimal fraction of the ORF length that overlaps a genomic feature to annotate the ORF as overlapping it.
(Default: 70%).
(See the Overlap section for more details).
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-out
Output directory.
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--show-types
Prints all genomic features annotated in the input GFF file.
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--show-chrs
Prints all the seqIDs (usually corresponding to chromosome or contig IDs) present in the input GFF file.
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--ofasta
Writes amino acid and nucleotide FASTA files for ORFs.