This table summarizes file format conversion commands in USEARCH. If you need support for other formats, let me know.
| From format | To format | Command-line |
| FASTQ | FASTA | usearch -fastq_filter in.fastq -fastaout out.fasta |
| SAM | human-readable alignments | usearch -sam_filter in.sam -alnout out.aln |
| SAM | BLAST -outfmt 6 | usearch -sam_filter in.sam -blast6out out.b6 |
| UDB | FASTA | usearch -udb2fasta in.udb -fastaout out.fasta |
| FASTA | UDB | see makeudb_ublast, makeudb_usearch. |