# A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

## Documentation for package ‘FastqCleaner’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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