annot command
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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



annot command

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