findorfs command
The fastx_findorfs command finds ORFs in nucleotide sequences in a FASTA or FASTQ file.
The - orfstyle and - mincodons options control ORF identification. The -output option specifies the output filename.
The - ntout output file is a FASTA filename for nucleotide sequences.
The - aaout output file is a FASTA filename for translated (amino acid) sequences.
Example
usearch -fastx_findorfs reads.fastq -ntout -nt.fa -aaout aa.fa -orfstyle 7 -mincodons 16
