debar {debar}R Documentation

debar

Description

debar is an R package designed for the identification and removal of insertion and deletion errors from COI-5P DNA barcode data.

Details

debar is built around the DNAseq object, which takes a COI-5P DNA barcode sequence and optionally its associated name and PHRED quality information as input. The package utilizes a nucleotide profile hidden Markov model (PHMM) for the identification of the COI-5P region of an input sequence and the identification and correction of indel errors from within the COI-5P region of the sequence. Indel corrections are by default applied in a conservative fashion, with subsequent censorship of 7 base pairs in either direction of an indel correction to mask most instances where the exact bp corresponding to the indel was not found exactly. Numerous filtering and double check steps are applied, and the package includes functions for input/output for either fasta or fastq formats.

The denoise pipeline is heavily paramaterized so that a user can tailor the denoising execution for their own data structure and goal.

Functions

Data

Author(s)

Cameron M. Nugent


[Package debar version 0.1.1 Index]