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findorfs command

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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