bactopia-search

Query against ENA and SRA for public accessions to process with Bactopia

Usage

bactopia-search [OPTIONS]

Required Options

Option	Type	Default	Description
--query, -q	STRING		Taxon ID or Study, BioSample, or Run accession (can also be comma separated or a file of accessions)

Query Options

Option	Type	Default	Description
--exact-taxon	BOOL	false	Exclude Taxon ID descendants
--limit, -l	INT	1000000	Maximum number of results (per query) to return
--accession-limit, -al	INT	5000	Maximum number of accessions to query at once
--biosample-subset	INT	0	If a BioSample has multiple Experiments, maximum number to randomly select (0 = disabled)
--include-empty	BOOL	false	Include metadata columns that are empty for all rows

Filtering Options

Option	Type	Default	Description
--min-base-count, -mbc	INT	0	Filters samples based on minimum base pair count (0 = disabled)
--min-read-length, -mrl	INT	0	Filters samples based on minimum mean read length (0 = disabled)
--min-coverage, -mc	INT	0	Filter samples based on minimum coverage (requires --genome_size, 0 = disabled)

Additional Options

Option	Type	Default	Description
--genome-size, -gsize	INT	0	Genome size to be used for all samples, and for calculating min coverage
--use-ncbi-genome-size	BOOL	false	If available, use NCBI genome size for species
--outdir, -o	STRING	./	Directory to write output
--prefix, -p	STRING	bactopia	Prefix to use for output file names
--force	BOOL	false	Overwrite existing reports
--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.