sanger_consensus

Description:

This function loads in the CSV results table from isoQC and merges related sequences based on user input. Original file names before isoQC step need to have a common prefix and differentiating suffixes. (e.g. SAMPLE_01_F.ab1, SAMPLE_01_R.ab1). After aligning paired sequences, the consensus sequence is extracted and priority is given to the read with higher quality. Phred quality scores are reassigned in the final output table in a basic way by taking the mean of both input sequences.

Note: This function is designed to be used after the isoQC step and before the isoTAX step.

Usage:

sanger_consensus(input=NULL,
                 suffix="_F.ab1|_R.ab1")

Arguments:

Parameter	Description
input	Path of CSV output file from isoQC step.
suffix	Regex-friendly suffix for denoting filename groupings. Default="_F.ab1|_R.ab1" for the common scenario of Sanger sequencing a marker gene in forward and reverse. Direction of sequences including reverse complements will be automatically detected.