| adapter_filter | Remove full and partial adapters from a ShortReadQ object |
| check_encoding | Check quality encoding |
| complex_filter | Remove sequences with low complexity |
| fixed_filter | Remove a fixed number of bases of a ShortReadQ object from 3' or 5' |
| inject_letter_random | Inject a letter in a set of sequences at random positions |
| launch_fqc | Launch FastqCleaner application |
| length_filter | Filter sequences of a FASTQ file by length |
| n_filter | Remove sequences with non-identified bases (Ns) from a ShortReadQ object |
| qmean_filter | Filter sequences by their average quality |
| random_length | Create a named object with random sequences and qualities |
| random_qual | Create random qualities for a given encoding |
| random_seq | Create random sequences |
| seq_filter | Remove a set of sequences |
| seq_names | Create sequences names |
| trim3q_filter | Filter sequences with low quality in 3' tails |
| unique_filter | Remove duplicated sequences in a FASTQ file |