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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_uniques_persample command

See also
fastx_uniques command

This command reports the set of unique sequences for each sample in the input file. Labels in the input file must have sample identifiers. If the same unique sequence is found in multiple samples, one output sequence is reported for each sample. Usually, the -sizeout option is used to specify the abundance of the unique sequence within the sample.

The effect of using this command is to compress the input dataset without losing sequence or sample information.

It is NOT VALID to use the output file from fastx_uniques_persample as input for OTU clustering (cluster_otus command) or denoising (unoise3 command).

It is ok to use the output file as the input for creating an OTU table using the otutab command.

Input can be in FASTA or FASTQ format. The output filename is specified by -fastqout (FASTQ format) and / or -fastaout (FASTA format). You cannot create FASTQ output from FASTA input.

The -sizeout option specifies that size annotations should be added to the output sequence labels.

The -minuniquesize option specifies the minimum size (unique sequence abundance) to output. Default 1.

The -topn N option specifies that at most N sequences should be output (requires v10.1 or later).


usearch -fastx_uniques_persample reads.fq -output uniques.fa -sizeout -minuniquesize 2