bactopia-check-fastqs

Verify input FASTQs meet minimum requirements.

Usage

bactopia-check-fastqs [OPTIONS]

Options

Option	Type	Default	Description
--version, -V	BOOL	false	Show the version and exit.
--sample	STRING		Name of the input sample.
--fq1	STRING		Stats for SE or R1 FASTQ in JSON format.
--fq2	STRING		Stats for R2 FASTQ in JSON format.
--min_proportion	FLOAT	0.0	Minimum basepair proportion for R1/R2.
--min_reads	INT	0	Minimum number of reads.
--min_basepairs	INT	0	Minimum number of sequenced basepairs.
--runtype	STRING	illumina	The input technology of the FASTQs.