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

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

## Documentation for package ‘debar’ version 0.1.1

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

## Help Pages

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.