Annotate reads from a marker gene sequencing experiment. Can be used for mock communities 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, typically these are reference sequences for a mock community. One or both of -knowndb and -db can be specified.
-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 community experiments to enable detection of contaminants.
One or both of -knowndb and -db can be specified.
-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
usearch -annot mock_reads.fq -knowndb mock_ref.fa -db silva.udb
-tabbedout annot.txt -fastqout annot.fq