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fastx_getseq command
Commands > FASTA/Q files

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Extract one or more sequences from a FASTA or FASTQ file. The label is given by the -label option. Only one -label option may be specified.

If the ‑label_substr_match option is specified, then the label given on the command-line may be a substring of a sequence label, which may result in more than one sequence being extracted.

Output is written to -fastaout (FASTA) and/or -fastqout (FASTQ). You cannot use -fastqout if the input is FASTA because the quality scores are not known.


usearch -fastx_getseq reads.fa -label FO09O1002IH8ZO -fastqout the_read.fq -fastaout the_read.fa

usearch -fastx_getseq genome.fa -label chromosome_3 -fastaout chr3.fa