| 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) |