annot command
Annotate reads from a marker gene sequencing experiment. Can be used for mock community and "real" communities. Classifies reads as known sequence, known sequences with error, PhiX, chimera etc.
-knowndb option: database file (udb or FASTA) with sequences expected to be in the reads, typical use is the reference sequences for a mock community.
-db option: database file (udb or FASTA), should be the largest available database for the gene e.g. SILVA for 16S or UNITE for ITS. Should be provided for mock communitiy experiments to enable detection of contaminants.
-tabbedout option. Tabbed text output file with one line per input sequence.
-fastaout option. FASTA output file, annotation is added to the sequence labels.
-fastqout option. FASTQ output file, annotation is added to the sequence labels.
Multithreading is supported
Example
usearch -annot mock_reads.fq -knowndb mock_ref.fa -db silva.fa -tabbedout
annot.txt -fastqout annot.fq