A Post-Clustering Denoiser for COI-5P Barcode Data

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Documentation for package ‘debar’ version 0.1.1

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debar-package 'debar'
aa_check Translate the sequence and it for stop codons
aa_check.DNAseq Translate the sequence and it for stop codons
adjust Adjust the sequences based on the nt path outputs.
adjust.DNAseq Adjust the sequences based on the nt path outputs.
censored_translation Censored Translation of a DNA string.
consensus Take the list of denoised sequences and obtain the consensus sequence.
consensus_sequence Take the list of denoised sequences and obtain the consensus sequence.
debar 'debar'
denoise Run the denoiser pipeline for a sequence read.
denoise.default Run the denoiser pipeline for a sequence read.
denoise_file Denoise sequence data from a given file.
denoise_file.default Denoise sequence data from a given file.
denoise_list List-to-list denoising of COI barcode sequences.
dir_check Take an input sequence and align both the forward and reverse compliments to the PHMM
DNAseq Build a DNAseq object from a DNA sequence string.
example_nt_string Example coi5p DNA sequence string.
example_nt_string_errors Example coi5p DNA sequence string with insertion and deletion errors.
ex_nt_list An example of a list of four coi5p sequences, each containing indel errors.
frame Take a DNAseq object and isolate the COI-5P region.
frame.DNAseq Take a DNAseq object and isolate the COI-5P region.
outseq Get the final denoised output sequence for a read.
outseq.DNAseq Get the final denoised output sequence for a read.
read_fasta Read in raw data from a fasta file.
read_fastq Read in raw data from a fastq file.
write_fasta Output the denoised consensus sequence to a fasta file.
write_fasta.DNAseq Output the denoised consensus sequence to a fasta file.
write_fastq Output the denoised sequence to a fastq format with placeholder phred scores.
write_fastq.DNAseq Output the denoised sequence to a fastq format with placeholder phred scores.