Commands > Clustering, FASTA/Q files, Reads
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
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