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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.



fastx_learn command

See also
unoise3 command

Determines error rates of amplicon reads. Input is a set of unique sequences with size=annotations. The input file is usually generated by the fastx_uniques command with the -sizeout option. It can be in FASTQ or FASTA format. If FASTQ format is provided, then the expected errors predicted by the Q scores are compared with the measured error rates, and the accuracy of the Q scores is measured by comparing the observed and predicted error rate for each value of Q. Click here for an example report.

This command is useful for checking the error rate after expected error quality filtering, which assumes that the Q scores are accurate. It does not use Q scores so gives an indpendent check.

The -output option specifies a text file to contain the report.


usearch -fastx_learn uniques.fastq -output learn.txt