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 genome.fasta --gff genome.gff --singularity

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).

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 inout GFF)(e.g. chromosome I) with the following instruction:

orftrack --fna genome.fasta --gff genome.gff  --chr seqID --singularity 

in this example :

orftrack --fna genome.fasta --gff genome.gff  --chr I --singularity 

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 genome.fasta --gff genome.gff  --chr seqID1 seqID2 seqIDx --singularity