See also
fastx_getseq
fastx_getsubseq
Extract sequences from a FASTA or FASTQ file. The labels are given in a file specified by the -labels option. The labels file is a text file with one label per line. There should be no other characters, e.g. white space (blank or tabs) in a line.
Output is written to filenames given by -fastaout (FASTA) and/or -fastqout (FASTQ). You cannot use -fastqout if the input is FASTA because the quality scores are not known.
Sequences which do not match are written to filename given by -notmatched (FASTA).
If the ‑label_substr_match option is specified, then the labels in the labels file may be substrings of the sequence labels.
Example
usearch -fastx_getseqs reads.fq -labels labels.txt -fastaout
reads_subset.fa