Get read quality summary statistics from fastp
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)