Annotation of ORFs with ORFtrack#

Running ORFtrack on a complete genome#

The following instruction annotates all the possible ORFs of the input genome.

orftrack -fna /database/genome.fasta -gff /database/genome.gff

Depending on the size of the genome, ORFtrack takes a few minutes to several hours to annotate all the ORFs of a genome. It returns a new gff file containing the annotation of all the identified ORFs (including coding and noncoding ORFs). The output gff file is stored in the /database/ folder of the container and named mapping_orf_[genome].gff. It also provides a summary.log file that summarizes for each chromosome/contig all the ORF categories that have been detected.

Running ORFtrack on a single chromosome or a subset of chromosomes#

ORFtrack can be launched on a single seqID (usually chromosome or contig indicated in the first column of the input gff)(e.g. chromosome seqID: XXX) with the following instruction:

orftrack -fna /database/genome.fasta -gff /database/genome.gff  -chr chr_ID_XXXX

This can be very useful if the user wants to run ORFtrack on several CPUs. Also, it can be launched on a subset of seqIDs as follows:

orftrack -fna /database/genome.fasta -gff /database/genome.gff  -chr seqID1 seqID2 seqIDx