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File format conversions

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.