summary_stats_fastp: Get read quality summary statistics from fastp

View source: R/02_qc.R

summary_stats_fastpR Documentation

Get read quality summary statistics from fastp

Description

Get read quality summary statistics from fastp

Usage

summary_stats_fastp(fastp_qcdir = "results/QC_dir/fastp_stats")

Arguments

fastp_qcdir

Character with path to the directory where .json files from fastp are stored. Default: results/QC_dir/fastp_stats.

Value

A data frame of fastp summary stats for each sample with the following variables:

  • Sample

  • sequencing

  • before_nreads

  • before_nbases

  • before_q20bases

  • before_q30bases

  • before_q20rate

  • before_q30rate

  • before_GCcontent

  • before_meanlength

  • after_nreads

  • after_nbases

  • after_q20bases

  • after_q30bases

  • after_q20rate

  • after_q30rate

  • after_GCcontent

  • after_meanlength

  • filter_n_passed

  • filter_n_lowquality

  • filter_n_too_many_N

  • filter_n_tooshort

  • filter_n_toolong

  • duplication_rate

Examples

fastp_qcdir <- system.file("extdata", package = "bears")
fastp_stats <- summary_stats_fastp(fastp_qcdir)

almeidasilvaf/gead documentation built on April 26, 2023, 3:47 p.m.