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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