Man pages for debar
A Post-Clustering Denoiser for COI-5P Barcode Data

aa_checkTranslate the sequence and it for stop codons
adj_seqAdjust the DNA sequence based on the ntPHMM path
adjustAdjust the sequences based on the nt path outputs.
censored_translationCensored Translation of a DNA string.
col_modeDetermining the most common character in each column.
consensusTake the list of denoised sequences and obtain the consensus...
denoiseRun the denoiser pipeline for a sequence read.
denoise_fileDenoise sequence data from a given file.
denoise_listList-to-list denoising of COI barcode sequences.
dir_checkTake an input sequence and align both the forward and reverse...
DNAseqBuild a DNAseq object from a DNA sequence string.
example_nt_stringExample coi5p DNA sequence string.
example_nt_string_errorsExample coi5p DNA sequence string with insertion and deletion...
ex_nt_listAn example of a list of four coi5p sequences, each containing...
frameTake a DNAseq object and isolate the COI-5P region.
individual_DNAbinbuild an DNAbin with ape.
ins_front_trimcheck sequence for an early large string of deletions, if it...
leading_insCheck for a large number of leading inserted bases, if this...
meta_checkRun the log file and reject processing code after running the...
new_DNAseqBuild a new DNAseq class instance.
nt_PHMMNucleotide profile hidden markov model for debar.
outseqGet the final denoised output sequence for a read.
print.DNAseqPrint a concise summary of the DNAseq object
read_fastaRead in raw data from a fasta file.
read_fastqRead in raw data from a fastq file.
rev_compReturn the reverse compliment for a DNA sequence
set_frameTake an input sequence and get it into the reading frame....
translate_codonCensored Translation of a codon.
triple_delsLook for triple deletes in the PHMM path.
triple_insLook for triple inserts in the PHMM path.
validate_DNAseqValidate the new DNAseq class instance.
write_fastaOutput the denoised consensus sequence to a fasta file.
write_fastqOutput the denoised sequence to a fastq format with...
write_wrapperA wrapper function to deploy the fastq and fata output...
debar documentation built on Jan. 11, 2020, 9:31 a.m.