seqDepth: Calculating sequencing depths from the output of 'seqkit...
In wanyuac/handyR: Handy functions for R programming.

seqDepth

R Documentation

Calculating sequencing depths from the output of 'seqkit stats'

This function calculates the sequencing depth of each genome using the output of command 'seqkit stats' (https://github.com/shenwei356/seqkit)

seqDepth(reads, len, srt = TRUE)

`reads`	A data frame imported from the output file of 'seqkit stats'. The first column of input file names must not contain paths. For example, sample_1.fastq.gz is valid whereas reads/filtered/sample_1.fastq.gz is invalid. Each FASTQ file should follow the pattern *_1, 2.fastq.gz.
`len`	Length (bp) of the reference genome
`srt`	Whether to sort rows by sequencing depths (default: TRUE)