| aa_check | Translate the sequence and it for stop codons |
| adj_seq | Adjust the DNA sequence based on the ntPHMM path |
| adjust | Adjust the sequences based on the nt path outputs. |
| censored_translation | Censored Translation of a DNA string. |
| col_mode | Determining the most common character in each column. |
| consensus | Take the list of denoised sequences and obtain the consensus... |
| debar | 'debar' |
| denoise | Run the denoiser pipeline for a sequence read. |
| denoise_file | 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... |
| 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... |
| ex_nt_list | An example of a list of four coi5p sequences, each containing... |
| frame | Take a DNAseq object and isolate the COI-5P region. |
| individual_DNAbin | build an DNAbin with ape. |
| ins_front_trim | check sequence for an early large string of deletions, if it... |
| leading_ins | Check for a large number of leading inserted bases, if this... |
| meta_check | Run the log file and reject processing code after running the... |
| new_DNAseq | Build a new DNAseq class instance. |
| nt_PHMM | Nucleotide profile hidden markov model for debar. |
| outseq | Get the final denoised output sequence for a read. |
| print.DNAseq | Print a concise summary of the DNAseq object |
| read_fasta | Read in raw data from a fasta file. |
| read_fastq | Read in raw data from a fastq file. |
| rev_comp | Return the reverse compliment for a DNA sequence |
| set_frame | Take an input sequence and get it into the reading frame.... |
| translate_codon | Censored Translation of a codon. |
| triple_dels | Look for triple deletes in the PHMM path. |
| triple_ins | Look for triple inserts in the PHMM path. |
| validate_DNAseq | Validate the new DNAseq class instance. |
| write_fasta | Output the denoised consensus sequence to a fasta file. |
| write_fastq | Output the denoised sequence to a fastq format with... |
| write_wrapper | A wrapper function to deploy the fastq and fata output... |
