binSeqErr_internal: Computes the sequencing error rate for each bin

In philliplab/MotifBinner2: Processes NGS Primer ID Datasets

Description

Under the assumption that there was zero PCR recombination and no PID collisions, the only source of heterogeneity in the bins are sequencing errors. Thus a comparison between each read in a bin and the bin's consensus sequence can be taken as an indication of the sequencing error rates.

Usage

binSeqErr_internal(cons_dat, msa_dat)

Arguments

cons_dat	The consensus sequences. Their names must start with the PID followed by an underscore and then anything.
msa_dat	The reads with sequences of each bin aligned. The sequence name must contain PID:_ followed by the PID somewhere in the name.

Details

A full characterization of the errors is returned that tallies each match and mismatch and the quality at which they happened.

philliplab/MotifBinner2 documentation built on Sept. 8, 2020, 12:09 a.m.