All functions

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