| Format | Description | |
| Database files | Target sequences plus possible index. | |
| UDB | USEARCH database with sequences and index. | |
| FASTA | Text file containing sequence data. | |
| FASTQ | Text file containing sequence data and quality scores. | |
| SAM | Alignment format used by read mappers. | |
| Labels | Sequence labels, see also size annotations and ‑notrunclabels option. | |
| blast6out | Tabbed text compatible with BLAST -m8 and BLAST+ -outfmt 6. | |
| Labels | Sequence labels, see also size annotations and ‑notrunclabels option. |