| derep_fulllength | Find unique sequences and abundances (old name for fastx_uniques) | |
| fastq_chars | Reports frequencies of Phred (Q) scores in FASTQ file | |
| fastq_eestats | Expected error distribution in FASTQ file (long report) | |
| fastq_eestats2 | Expected error distribution in FASTQ file (short report) | |
| fastq_filter | Quality filter FASTQ and/or convert reads to FASTA format. | |
| fastq_join | Concatenate forward (R1) and reverse (R2) reads | |
| fastq_mergepairs | Merge (assemble) paired reads with overlaps | |
| fastq_sra_splitpairs | Recover R1 and R2 reads from SRA interleaved or concatenated format | |
| fastx2qiime | Convert sample names to QIIME-compatible format | |
| fastx_demux | Assign reads to samples using index reads (demultiplex) | |
| fastx_learn | Estimate error rates for amplicon reads | |
| 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 | |
| orient | Orient nt sequences to the same strand as a database | |
| sortbylength | Sort by decresing sequence length | |
| sortbysize | Sort by decresing abundance (size= annotations) | |
| unoise3 | Correct errors (denoise) amplicon reads, includes chimera filter |