bactopia-prepare

Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia

Usage

bactopia-prepare [OPTIONS]

Required Options

Option	Type	Default	Description
--path, -p	STRING		Directory where FASTQ files are stored

Matching Options

Option	Type	Default	Description
--assembly-ext, -a	STRING	.fna.gz	Extension of the FASTA assemblies
--fastq-ext, -f	STRING	.fastq.gz	Extension of the FASTQs
--fastq-separator	STRING	_	Split FASTQ name on the last occurrence of the separator
--pe1-pattern	STRING	`[Aa]	[Rr]1
--pe2-pattern	STRING	`[Bb]	[Rr]2
--merge	BOOL	false	Flag samples with multiple read sets to be merged by Bactopia
--ont	BOOL	false	Single-end reads should be treated as Oxford Nanopore reads
--hybrid	BOOL	false	Samples with paired and single-end reads will be set to Illumina-first hybrid assembly (requires --ont)
--short-polish	BOOL	false	Samples with paired and single-end reads will be set to Nanopore-first hybrid assembly (requires --ont)
--recursive, -r	BOOL	false	Directories will be traversed recursively
--prefix	STRING		Prefix to add to the path

Sample Information Options

Option	Type	Default	Description
--metadata	STRING		Metadata per sample with genome size and species information
--genome-size, -gsize	INT	0	Genome size to use for all samples
--species, -s	STRING	UNKNOWN_SPECIES	Species to use for all samples (If available, can be used to determine genome size)
--taxid	STRING		Use the genome size of the Taxon ID for all samples

Additional Options

Option	Type	Default	Description
--examples	BOOL	false	Print example usage
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed
--version, -V	BOOL	false	Show the version and exit.