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FASTA/Q files
derep_fulllength Find unique sequences and abundances (old name for fastx_uniques)
fasta_explode Split FASTA into one file per sequence
fasta_stripgaps Strip gap characters from sequences
fastx2qiime Convert sample names to QIIME-compatible format
fastx_demux Assign reads to samples using index reads (demultiplex)
fastx_findorfs Find Open Reading Frames (ORFs) in FASTX file
fastx_getlabels Get labels from FASTA/Q file
fastx_getseq Extract sequence(s) by label from FASTX file
fastx_getseqs Extract sequence(s) by label from FASTX file
fastx_getsubseq Extract subsequence by label and start-stop coordinates from FASTX file
fastx_info Summarize contents of FASTX file
fastx_learn Estimate error rates for amplicon reads
fastx_mask Low-complexity masking
fastx_relabel Re-label FASTA/Q sequences
fastx_revcomp Reverse-complement nucleotide sequences
fastx_split Split FASTX file into two or more roughly equal-size pieces
fastx_strip_annots Strip annotations from labels
fastx_subsample Extract random subset of sequences in a FASTX file
fastx_truncate Truncate sequences
fastx_uniques Find unique sequences and abundances
fastx_uniques_persample Find unique sequences and abundances per sample
filter_phix Filter PhiX sequences
sortbylength Sort by decresing sequence length
sortbysize Sort by decresing abundance (size= annotations)