ORFtrack parameters#

Mandatory

-fna nucleotide fasta file of the genome whose ORFs are to annotate

-gff gff annotation file

Optional

-h, --help shows the help and exits

--show-types prints all genomic features annotated in the input gff file

--show-chrs prints all the seqID (usually corresponding to chromosome or contig ID) present in the input gff file

-chr list of seqID to be treated by ORFtrack (i.e. column #1 of the gff file - generally chromosome or contig ID). ID must be separated by a space: -chr NC_001148.4 NC_001139.3
In this case, ORFtrack will not treat the entire genome, but the following seqID NC_001148.4 NC_001139.3. We recommend using this option when dealing with large genomes in order to distribute the calculations on several CPUs (one per (subset of) seqID).

-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).

-co_ovp Minimal fraction of the ORF length that overlaps a genomic feature to annotate the ORF as overlapping it (default: 0.70). (see the Overlap section for more details).

-types_only Genomic feature(s) considered for the annotation step ('CDS' is included by default). If there are several genomic features to be considered, they must be given separated by a space. Noncoding ORFs are annotated as intergenic (when they do not overlap any feature) or overlapping (when they overlap a given genomic feature). The "overlapping" status directly derives from the genomic features considered for the annotation step. For example, if the user specifies with the "types_only" option, the features "tRNA" and "rRNA" (CDS are included by default), all ORFs that overlap another genomic feature (i.e. different from tRNA, rRNA, or CDS) will be annotated as noncoding intergenic ORFs. If no genomic feature is indicated, noncoding ORFs that overlap any genomic feature annotated in the original gff file will be annotated as noncoding ORF overlapping the corresponding genomic feature. Nevertheless, the resulting ORFs can be treated specifically (grouped according to their annotation for example) with ORFget afterwards (see the ORFget section for more details).

-types_except Genomic feature(s) not to be considered for the annotation step ('gene' and 'exon' not considered by default). If there are several genomic features to be considered, they must be given separated by a space. Noncoding ORFs are annotated as intergenic (when they do not overlap any feature) or overlapping (when they overlap a given genomic feature). The "overlapping" status directly derives from the genomic features considered for the annotation step. For example, when specifying with the "types_except" option, the features "telomer" and "centromer" ('gene' and 'exon' not considered by default), if an ORF overlaps a "telomer", "centromer", "gene" and/or "exon", the overlap will not be considered and the ORF will be annotated as intergenic or overalapping another genomic feature if there is another genomic feature in the same region (e.g. an ORF that overlaps at the same time a gene and a tRNA will be annotated as overlapping a tRNA since the gene is not considered for the ORF annotation). If no genomic feature is indicated, noncoding ORFs that overlap any genomic feature annotated in the original gff file will be annotated as noncoding ORF overlapping the corresponding genomic feature. Nevertheless, the resulting ORFs can be treated specifically (grouped according to their annotation for example) with ORFget afterwards (see the ORFget section for more details).