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


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Documentation for package ‘FastqCleaner’ version 1.24.0

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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