quality_control: Workflow for basic quality assessment of the read files.

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

Workflow for basic quality assessment of the read files.

Description

Workflow for basic quality assessment of the read files.

Usage

quality_control(object, min_score = 10, n = 10000)

Arguments

object	An experiment data table as returned by find_read_files or a worflow object.
min_score	The smallest quality score still considered okayish.
n	Largest number of reads for each file. Will be sampled if more are found.

Value

A list with the following elements:

files

The input files to produce the report

qualities

data table of qualities scores per cycle and sample

bases

data table of base calls per cycle and sample

quality_plot

sample quality profiles

length_plot

distribution of cycles that pass the quality cutoff

entropy_plot

sample base entropy

Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.