Man pages for compbiocore/qckitfastq
FASTQ Quality Control
| adapter_content | Creates a sorted from most frequent to least frequent... |
| calc_adapter_content | Compute adapter content in reads. This function is only... |
| calc_format_score | Calculate score based on Illumina format |
| calc_over_rep_seq | Calculate sequece counts for each unique sequence and create... |
| dimensions | Extract the number of columns and rows for a FASTQ file using... |
| find_format | Gets quality score encoding format from the FASTQ file.... |
| GC_content | Calculates GC content percentage for each read in the... |
| gc_per_read | Calculate GC nucleotide sequence content per read of the... |
| kmer_count | Return kmer count per sequence for the length of kmer desired |
| overrep_kmer | Generate overrepresented kmers of length k based on their... |
| overrep_reads | Sort all sequences per read by count. |
| per_base_quality | Compute the mean, median, and percentiles of quality score... |
| per_read_quality | Compute the mean quality score per read. 'per_read_quality' |
| plot_adapter_content | Creates a bar plot of the top 5 most present adapter... |
| plot_GC_content | Generate mean GC content histogram. |
| plot_outliers | Determine how to plot outliers. Heuristic used is whether... |
| plot_overrep_kmer | Create a box plot of the log2(observed/expected) ratio across... |
| plot_overrep_reads | Plot the top 5 seqeunces |
| plot_per_base_quality | Generate a boxplot of the per position quality score. |
| plot_per_read_quality | Plot the mean quality score per sequence as a histogram. High... |
| plot_read_content | Plot the per position nucleotide content. |
| plot_read_length | Plot a histogram of the number of reads with each read... |
| qual_score_per_read | Calculate the mean quality score per read of the FASTQ... |
| read_base_content | Compute nucleotide content per position for a single base... |
| read_content | Compute nucleotide content per position. Wrapper function... |
| read_length | Creates a data frame of read lengths and the number of reads... |
| run_all | Will run all functions in the qckitfastq suite and save the... |
