Commands for sequences in FASTx format (FASTA and FASTQ)
allpairs_global Align all pairs in FASTx file using global alignment
allpairs_local Align all pairs in FASTx file using local alignment
fasta_explode De-unique FASTA file with size=nnn annotations
fasta_stripgaps Remove gap symbols from FASTA file
fastx2qiime Convert sample labels from usearch to QIIME format
fastx_demux Assign reads to samples (demultiplex)
fastx_findorfs Identify ORFs in nucleotide sequences
fastx_get_sample_names Extract sample names from FASTx file
fastx_getlabels Extract sequence labels from FASTx file
fastx_getseq Extract sequence(s) matching label
fastx_getseqs Extract sequence(s) matching labels
fastx_getsubseq Extract subsequence given label, start, stop
fastx_info Report summary information about a FASTx file
fastx_learn Estimate error rates from amplicon reads
fastx_mask Mask low-complexity sequence
fastx_relabel Re-label sequences in FASTx file with prefix plus sequential number
fastx_revcomp Reverse-complement nucleotide sequence
fastx_split Divide sequences in FASTx file into given number of files
fastx_strip_annots Remove usearch-style annotations (name=xxx) from FASTx file
fastx_subsample Extract random sub-sample from FASTx file
fastx_syncpairs Sort forward and reverse reads into the same order
fastx_trim_primer Remove primer-binding sequence from FASTx file
fastx_truncate Truncate sequences in FASTx file
fastx_uniques Identify unique sequences in FASTx file (dereplicate)
fastx_uniques_persample Identify unique sequences per sample in FASTx file
filter_lowc Filter low-complexity sequences from FASTx file
filter_phix Remove PhiX spike sequences from FASTx file
sortbylength Sort sequences in FASTx file by decreasing length
sortbysize Sort sequences in FASTx file by decreasing size=nnn